01.00-trimming-fastp-fastqc-multiqc ================ Sam White 2025-04-17 - [1 BACKGROUND](#1-background) - [2 Set R variables](#2-set-r-variables) - [3 Fastp Trimming](#3-fastp-trimming) - [4 FastQC/MultiQC on trimmed reads](#4-fastqcmultiqc-on-trimmed-reads) - [4.1 Create FastQ list to use across chunks](#41-create-fastq-list-to-use-across-chunks) - [4.2 Run FastQC/MultiQC](#42-run-fastqcmultiqc) - [4.3 List output files](#43-list-output-files) # 1 BACKGROUND This Rmd file trims FastQ files using [fastp](https://github.com/OpenGene/fastp) (Chen 2023), followed by quality checks with [FastQC](https://github.com/s-andrews/FastQC) and [MultiQC](https://multiqc.info/) (Ewels et al. 2016). Additionally, it renames the trimmed FastQ files to be compliant with QIIME 2 naming expectations.
If you need to download the raw sequencing reads, please see [00.00-fastqc-multiqc-raw-reads.Rmd](https://github.com/RobertsLab/project-eDNA-yellow/blob/2cf2f152dd2a416360752a72c1bf2602d28cdd03/code/00.00-fastqc-multiqc-raw-reads.Rmd)
Inputs: - Paired-end FastQs - Example filename format: `Yell_July18_Site1f_S92_L001_R[12]_001.fastq.gz` Outputs: - Trimmed FastQs. - Example filename format: `Site1z_S129_L001_R1_001.fastq.gz` - fastp JSON files. - FastQC HTML files. - MultiQC HTML report. Software requirements: - [fastp](https://github.com/OpenGene/fastp) - [FastQC](https://github.com/s-andrews/FastQC) - [MultiQC](https://github.com/MultiQC/MultiQC) (Ewels et al. 2016) # 2 Set R variables ``` r # Data directories repo_dir <- "/home/sam/gitrepos/RobertsLab/project-eDNA-yellow" data_dir <- file.path(repo_dir, "data") raw_reads_dir <- file.path(data_dir, "raw-fastqs") output_dir <- file.path(repo_dir, "output", "01.00-trimming-fastp-fastqc-multiqc") # PROGRAMS fastp <- "/home/sam/programs/fastp" fastqc <- "/home/sam/programs/FastQC-0.12.1/fastqc" multiqc <- "/home/sam/programs/miniforge3/bin/multiqc" # CPUs threads <- 4 # Define file patterns R1_fastq_pattern <- "*_R1_001.fastq.gz" R2_fastq_pattern <- "*_R2_001.fastq.gz" # Export these as environment variables for bash chunks. Sys.setenv( fastp = fastp, fastqc = fastqc, data_dir = data_dir, multiqc = multiqc, raw_reads_dir = raw_reads_dir, threads = threads, R1_fastq_pattern = R1_fastq_pattern, R2_fastq_pattern = R2_fastq_pattern, output_dir = output_dir ) ``` # 3 Fastp Trimming [fastp](https://github.com/OpenGene/fastp) (Chen 2023) is set to auto-detect Illumina adapters, as well as trim the first 10bp from each read, as past experience shows these first 10bp are more inconsistent than the remainder of the read length.
Appends `_L001` to trimmed filenames for downstream QIIME 2 filename parsing requirements.
``` bash # Make output directories, if it doesn't exist mkdir --parents "${output_dir}" # Change to raw reads directory cd "${raw_reads_dir}" # Initialize metadata file for QIIME2 usage printf "%s\t%s\n" "id" "site" > metadata.tsv # Create arrays of fastq R1 files and sample names # Renames to match QIIME2 regex # Adds id to metadata TSV file for fastq in ${R1_fastq_pattern} do # Extract site information from filename using awk site=$(echo "${fastq}" | awk -F'_' '{print $3}') # Check if site information was extracted if [[ -n "${site}" ]]; then site_name=$(echo "$site" | sed 's/Site//') echo -e "${site}\t${site_name}" >> metadata.tsv else echo "Site information not found in filename: ${fastq}" fi fastq_array_R1+=("${fastq}") R1_names_array+=("$(echo "${fastq}" | awk -F'_' '{print $3"_"$4"_L001"}')") done # Create array of fastq R2 files # Renames to match QIIME2 regex for fastq in ${R2_fastq_pattern} do fastq_array_R2+=("${fastq}") R2_names_array+=("$(echo "${fastq}" | awk -F"_" '{print $3"_"$4"_L001"}')") done # Create list of fastq files used in analysis # Create MD5 checksum for reference if [ ! -f "${output_dir}"/raw-fastq-checksums.md5 ]; then for fastq in *.gz do md5sum "${fastq}" >>"${output_dir}"/raw-fastq-checksums.md5 done fi # Run fastp on files # Adds JSON report output for downstream usage by MultiQC for index in "${!fastq_array_R1[@]}" do R1_sample_name=$(echo "${R1_names_array[index]}") R2_sample_name=$(echo "${R2_names_array[index]}") ${fastp} \ --in1 ${fastq_array_R1[index]} \ --in2 ${fastq_array_R2[index]} \ --detect_adapter_for_pe \ --trim_front1 20 \ --trim_front2 20 \ --trim_poly_g \ --thread ${threads} \ --html "${output_dir}"/"${R1_sample_name}".fastp-trim.report.html \ --json "${output_dir}"/"${R1_sample_name}".fastp-trim.report.json \ --out1 "${output_dir}"/"${R1_sample_name}"_R1_001.fastq.gz \ --out2 "${output_dir}"/"${R2_sample_name}"_R2_001.fastq.gz \ 2>> "${output_dir}"/"${R1_sample_name}"-fastp.stderr # Generate md5 checksums for newly trimmed files cd "${output_dir}" md5sum "${R1_sample_name}"_R1_001.fastq.gz | tee "${R1_sample_name}"_R1_001.fastq.gz.md5 md5sum "${R2_sample_name}"_R2_001.fastq.gz | tee "${R2_sample_name}"_R2_001.fastq.gz.md5 # Change back to previous directory # Directing to /dev/null prevents printing directory each time. cd - > /dev/null done ``` 8aaf71fac78f18293155870a5ad785b3 Site1a_S83_L001_R1_001.fastq.gz 97674b5c315b18b1d65dd703301f0cf8 Site1a_S83_L001_R2_001.fastq.gz 8581bbf93dbe9a7c6a6443568b11eaf2 Site1bb_S139_L001_R1_001.fastq.gz 9cac6084d18a18fdd2344a9a57b10403 Site1bb_S139_L001_R2_001.fastq.gz 1246b72b4824c37e054859390148991e Site1b_S84_L001_R1_001.fastq.gz 1bb8c2f3a716a93e126b963ea4cace7a Site1b_S84_L001_R2_001.fastq.gz e1d79f610c9d4ab430fa87164682cd5d Site1cc_S140_L001_R1_001.fastq.gz 0b639417f1e158661096cd2b22de528d Site1cc_S140_L001_R2_001.fastq.gz ee1d281b609e1d0ba856594379cce5ab Site1c_S85_L001_R1_001.fastq.gz 206313466fc3767486648dd9389461d9 Site1c_S85_L001_R2_001.fastq.gz 9541e0f8ef84c5e84f6ea651f6791b58 Site1dd_S141_L001_R1_001.fastq.gz f47df7e27b542984de111c8cd7723bc0 Site1dd_S141_L001_R2_001.fastq.gz 53387ef241a3e8c0143841871ca9dfd2 Site1d_S86_L001_R1_001.fastq.gz 97ada736a1c7a8443f3767735a3f4af2 Site1d_S86_L001_R2_001.fastq.gz be2502232114fbb0e8d90566e19eb3bd Site1ee_S142_L001_R1_001.fastq.gz 5261ca016825c7b5d450dfbe01c60768 Site1ee_S142_L001_R2_001.fastq.gz 25a8c59b65537de78c48631eb06b510e Site1e_S91_L001_R1_001.fastq.gz 4e822610766ef7ba0edff4b006a2399a Site1e_S91_L001_R2_001.fastq.gz 515a2c77896fcd68ab258ac0cd8eab2a Site1f_S92_L001_R1_001.fastq.gz f2698536a899157de64bdd209c1da4e1 Site1f_S92_L001_R2_001.fastq.gz dbf74d130be8e07cd002098f37a035fe Site1g_S93_L001_R1_001.fastq.gz 0c3ce2ce7409f9336ca794235d11bda3 Site1g_S93_L001_R2_001.fastq.gz 6f0cf41ff0621d8cf3e0b8c556b77e50 Site1h_S94_L001_R1_001.fastq.gz a4d6e23c32fb28b0498f0b244ee91a79 Site1h_S94_L001_R2_001.fastq.gz 4829027bca04743495259631a1b1eca3 Site1J_S99_L001_R1_001.fastq.gz 4cadf419f24f0a2c0f3233372e6ea64e Site1J_S99_L001_R2_001.fastq.gz a83ad57c90291aa2017d2537635e66f8 Site1k_S100_L001_R1_001.fastq.gz 7454d28afadb600434f4496ad632e12c Site1k_S100_L001_R2_001.fastq.gz 06acae67aeb668d5b4fec20beb69c98a Site1L_S101_L001_R1_001.fastq.gz 5a50bf8f326a11caa43bc70730faa1c5 Site1L_S101_L001_R2_001.fastq.gz ba80095123abce2ab4663f0764512615 Site1m_S102_L001_R1_001.fastq.gz 5bf93acb6681d64c8d72217fc296c379 Site1m_S102_L001_R2_001.fastq.gz a75988d7ceb2c2b45961b758b45beb31 Site1n_S103_L001_R1_001.fastq.gz 6429f9f4b270c45a235f3c9692046de9 Site1n_S103_L001_R2_001.fastq.gz b0caaeb57060745075c54435aee49ac5 Site1o_S104_L001_R1_001.fastq.gz d22783c7530a0fdf873e872e07094746 Site1o_S104_L001_R2_001.fastq.gz f523c3b03f8812df8761f790ba623eac Site1p_S105_L001_R1_001.fastq.gz 03aea60308b0a2cff891b89eff355d2f Site1p_S105_L001_R2_001.fastq.gz 8f2eb5db49a151fe276fe171c542d047 Site1q_S106_L001_R1_001.fastq.gz 0cf20078b76b4347c94c3ae77b2661d7 Site1q_S106_L001_R2_001.fastq.gz 09732612243841b02949b81277d8c773 Site1r_S111_L001_R1_001.fastq.gz 38f855e73282ca882fdcee1403472e5d Site1r_S111_L001_R2_001.fastq.gz 593e0e7cfba4e5a68559b825b977242d Site1s_S112_L001_R1_001.fastq.gz 12d0370983ede990ddf2ac07b0cf758c Site1s_S112_L001_R2_001.fastq.gz 8f52b61eda289215c89485eec951e44f Site1t_S113_L001_R1_001.fastq.gz dc0fac87a5a4f5566dffa6613d53deb2 Site1t_S113_L001_R2_001.fastq.gz 30956b911fd2e2f24ab4ccc0c573731e Site1U_S114_L001_R1_001.fastq.gz cd55f7443d273282fa708a100178441f Site1U_S114_L001_R2_001.fastq.gz c4a3a5562592217bd7e8d00afef68aca Site1v_S117_L001_R1_001.fastq.gz 9045dec9d94aa7abae62f87c6aedf887 Site1v_S117_L001_R2_001.fastq.gz c5cf4558d20d7eb11005822f840fe5e9 Site1w_S118_L001_R1_001.fastq.gz 659fdc3781371ce4633158f3715b146d Site1w_S118_L001_R2_001.fastq.gz ffa9195d6deefec0c68545eb2414cc1e Site1y_S120_L001_R1_001.fastq.gz 6b4807441251796f88bfc296a5deca6b Site1y_S120_L001_R2_001.fastq.gz 9315432c107813a21c7957f2c0d08ed0 Site1z_S129_L001_R1_001.fastq.gz 10b325405136f1aed3f2893875c69f18 Site1z_S129_L001_R2_001.fastq.gz 5762e0cf30216d3e24d1c243f2558513 Site5aa_S132_L001_R1_001.fastq.gz f0953177a84c0f501415add9c873012f Site5aa_S132_L001_R2_001.fastq.gz a1930e5eb162b0ded2f02ce626ce6242 Site5a_S87_L001_R1_001.fastq.gz a89ee788797cb710e3ab81678aa960d2 Site5a_S87_L001_R2_001.fastq.gz ee7c34fc56c2792ad55c73e7f693460c Site5bb_S133_L001_R1_001.fastq.gz e7b8a722ed5f771772d31ce46d74e64f Site5bb_S133_L001_R2_001.fastq.gz 12fff50ad0731eb524d1f2201a247a64 Site5b_S88_L001_R1_001.fastq.gz 04740ff92fbe6ec1f4c16d52edfa410d Site5b_S88_L001_R2_001.fastq.gz 87a5ac12247a4f5c4e0638d031317bb9 Site5cc_S134_L001_R1_001.fastq.gz 80958be5b5221a1381db5fcdf05ba034 Site5cc_S134_L001_R2_001.fastq.gz f194b5e2f3e75418ed77679138f59837 Site5c_S89_L001_R1_001.fastq.gz 5ba8d21028e58b80c3e46cea97205877 Site5c_S89_L001_R2_001.fastq.gz 9a965e2bfb8749d21a1061d7e64771c8 Site5ee_S136_L001_R1_001.fastq.gz 721f85fe480672e7592133a4d844910e Site5ee_S136_L001_R2_001.fastq.gz d35dfb11147f6704f7ba8f2c51405497 Site5e_S95_L001_R1_001.fastq.gz 59b45bdec09b28dcbba42d2a5efbe3f9 Site5e_S95_L001_R2_001.fastq.gz 4d923a5e87234327ee4b75541e6753ee Site5ff_S137_L001_R1_001.fastq.gz 44bd520d27855eca3710239f1903b510 Site5ff_S137_L001_R2_001.fastq.gz 5d904b2b63cc83ee889e576dc2c31c34 Site5f_S96_L001_R1_001.fastq.gz c5214749a8a7350d94a569745eb4796d Site5f_S96_L001_R2_001.fastq.gz 3c3de33d88a1458ef44d1575cc7c0bc1 Site5g_S97_L001_R1_001.fastq.gz faafeab62cdcea2fa18e45c0d07eb39e Site5g_S97_L001_R2_001.fastq.gz 8189dd5b62d3bc273d44d3ecdbf2a30b Site5h_S98_L001_R1_001.fastq.gz b0a04485cd47f593d21bab691881526b Site5h_S98_L001_R2_001.fastq.gz 391361dbbea6ea843444d039e956281f Site5J_S107_L001_R1_001.fastq.gz f40eb23d525bbca759d4fdc4570e4ec7 Site5J_S107_L001_R2_001.fastq.gz c3da677478056c52a22cbe8d82ed549e Site5k_S108_L001_R1_001.fastq.gz 49b642aedc0ab037165e1f4d30deb3e6 Site5k_S108_L001_R2_001.fastq.gz a9990b1563964cd92cedd096fbae374c Site5L_S109_L001_R1_001.fastq.gz 3a373edc3a42fef99ff8cb2af598b083 Site5L_S109_L001_R2_001.fastq.gz 1ea2789de747a68f172b17b8a92ac9aa Site5m_S110_L001_R1_001.fastq.gz 3b09623221c7feee3ae437ed98daa793 Site5m_S110_L001_R2_001.fastq.gz d3dd601918da9a53e01652f55be56c9e Site5n_S115_L001_R1_001.fastq.gz 7a96bba9597b49560b217dc66dc4f7d1 Site5n_S115_L001_R2_001.fastq.gz 3742ec5d5da634361de9be32bbdac133 Site5o_S116_L001_R1_001.fastq.gz 5aa0261b0ba53542abe1e807cf3d7400 Site5o_S116_L001_R2_001.fastq.gz c3cb63e4427b5c701a09dc4c97ffde8f Site5p_S121_L001_R1_001.fastq.gz 5f5536f37eab281541d78f3474c6d7ae Site5p_S121_L001_R2_001.fastq.gz b647652678efc16348e43e911d73eca3 Site5q_S122_L001_R1_001.fastq.gz 58316f0b3d5422a97fd79e3710b60141 Site5q_S122_L001_R2_001.fastq.gz bc79ce422d33a70047caea95f20fb564 Site5r_S123_L001_R1_001.fastq.gz 0cbab3f554b88283f8221622fe7d90aa Site5r_S123_L001_R2_001.fastq.gz 0d20bf34943af844bfed49169993a818 Site5s_S124_L001_R1_001.fastq.gz f3c40f4d927c7a51d15cf05274be99fa Site5s_S124_L001_R2_001.fastq.gz 803db24bd314cd7e3d314b1b8f0b84b2 Site5u_S126_L001_R1_001.fastq.gz 2bc8d78ff999dd579c3753ade627c795 Site5u_S126_L001_R2_001.fastq.gz a24082a508d3d14c817e98a35eaf2130 Site5v_S127_L001_R1_001.fastq.gz 39ae4d0f9ea80fbd21ef798c9dd38086 Site5v_S127_L001_R2_001.fastq.gz de061e7ba1fe7e7f7b83bfc0912b0d02 Site5w_S128_L001_R1_001.fastq.gz 4c79dec89144623496dbab6c9dfa0252 Site5w_S128_L001_R2_001.fastq.gz dc899975947bf512f6402d888b59980b Site5z_S131_L001_R1_001.fastq.gz 73a4e01e0ef5b883e5529244bb7100bd Site5z_S131_L001_R2_001.fastq.gz # 4 FastQC/MultiQC on trimmed reads ## 4.1 Create FastQ list to use across chunks ``` r # Create the fastq list and string trimmed_fastqs_list <- list.files(path = Sys.getenv("output_dir"), pattern = "\\.fastq\\.gz$", full.names = TRUE) trimmed_fastqs_string <- paste(trimmed_fastqs_list, collapse = " ") # Update the environment variable with the actual string Sys.setenv(trimmed_fastqs_string = trimmed_fastqs_string) ``` ## 4.2 Run FastQC/MultiQC ``` bash # Make output directory if it doesn't exist mkdir --parents "${output_dir}" cd "${output_dir}" ############ RUN FASTQC ############ # Create array of trimmed FastQs # Access the individual FastQ files from the array IFS=' ' read -r -a trimmed_fastqs_array <<< "${trimmed_fastqs_string}" # Pass array contents to new variable as space-delimited list trimmed_fastqc_list=$(echo "${trimmed_fastqs_array[*]}") echo "Beginning FastQC on raw reads..." echo "" # Run FastQC ### NOTE: Do NOT quote trimmed_fastqc_list ${fastqc} \ --threads ${threads} \ --outdir ${output_dir} \ --quiet \ ${trimmed_fastqc_list} echo "FastQC on raw reads complete!" echo "" ############ END FASTQC ############ ############ RUN MULTIQC ############ echo "Beginning MultiQC on raw FastQC..." echo "" ${multiqc} --interactive \ ${output_dir} \ -o ${output_dir} echo "" echo "MultiQC on raw FastQs complete." echo "" ############ END MULTIQC ############ echo "Removing FastQC zip files." echo "" rm ${output_dir}/*.zip echo "FastQC zip files removed." echo "" ``` Beginning FastQC on raw reads... application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip application/gzip FastQC on raw reads complete! Beginning MultiQC on raw FastQC... /// MultiQC 🌏 v1.28 file_search | Search path: /home/sam/gitrepos/RobertsLab/project-eDNA-yellow/output/01.00-trimming-fastp-fastqc-multiqc fastp | Found 54 reports fastqc | Found 108 reports write_results | Data : multiqc_data write_results | Report : multiqc_report.html multiqc | MultiQC complete MultiQC on raw FastQs complete. Removing FastQC zip files. FastQC zip files removed. ## 4.3 List output files ``` bash cd "${output_dir}" ls -lh ``` total 1.3G drwxrwxr-x 2 sam sam 4.0K Apr 22 17:11 multiqc_data -rw-rw-r-- 1 sam sam 8.0M Apr 22 17:12 multiqc_report.html -rw-rw-r-- 1 sam sam 7.8K Apr 22 16:48 raw-fastq-checksums.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:49 Site1a_S83_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:49 Site1a_S83_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:49 Site1a_S83_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 922K Apr 22 17:10 Site1a_S83_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.7M Apr 22 16:49 Site1a_S83_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:49 Site1a_S83_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 914K Apr 22 17:10 Site1a_S83_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:49 Site1a_S83_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:49 Site1a_S83_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:49 Site1bb_S139_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:49 Site1bb_S139_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:49 Site1bb_S139_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 922K Apr 22 17:10 Site1bb_S139_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 7.0M Apr 22 16:49 Site1bb_S139_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:49 Site1bb_S139_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 932K Apr 22 17:10 Site1bb_S139_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 7.5M Apr 22 16:49 Site1bb_S139_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:49 Site1bb_S139_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:50 Site1b_S84_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:50 Site1b_S84_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 16:50 Site1b_S84_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 919K Apr 22 17:10 Site1b_S84_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.2M Apr 22 16:50 Site1b_S84_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:50 Site1b_S84_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 910K Apr 22 17:10 Site1b_S84_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 10M Apr 22 16:50 Site1b_S84_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:50 Site1b_S84_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:50 Site1cc_S140_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 16:50 Site1cc_S140_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 16:50 Site1cc_S140_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 924K Apr 22 17:10 Site1cc_S140_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 17M Apr 22 16:50 Site1cc_S140_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:50 Site1cc_S140_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 914K Apr 22 17:10 Site1cc_S140_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 19M Apr 22 16:50 Site1cc_S140_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:50 Site1cc_S140_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:51 Site1c_S85_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 16:51 Site1c_S85_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 16:51 Site1c_S85_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 932K Apr 22 17:10 Site1c_S85_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 6.8M Apr 22 16:51 Site1c_S85_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:51 Site1c_S85_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 937K Apr 22 17:10 Site1c_S85_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 7.4M Apr 22 16:51 Site1c_S85_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:51 Site1c_S85_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:51 Site1dd_S141_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:51 Site1dd_S141_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 16:51 Site1dd_S141_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 931K Apr 22 17:10 Site1dd_S141_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 19M Apr 22 16:51 Site1dd_S141_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:51 Site1dd_S141_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 935K Apr 22 17:10 Site1dd_S141_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 19M Apr 22 16:51 Site1dd_S141_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:51 Site1dd_S141_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:52 Site1d_S86_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:52 Site1d_S86_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:52 Site1d_S86_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 922K Apr 22 17:10 Site1d_S86_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.5M Apr 22 16:52 Site1d_S86_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:52 Site1d_S86_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 935K Apr 22 17:10 Site1d_S86_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:52 Site1d_S86_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:52 Site1d_S86_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:52 Site1ee_S142_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:52 Site1ee_S142_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:52 Site1ee_S142_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 944K Apr 22 17:10 Site1ee_S142_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 16:52 Site1ee_S142_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:52 Site1ee_S142_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 952K Apr 22 17:10 Site1ee_S142_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:52 Site1ee_S142_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 16:52 Site1ee_S142_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:52 Site1e_S91_L001-fastp.stderr -rw-rw-r-- 1 sam sam 484K Apr 22 16:52 Site1e_S91_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 170K Apr 22 16:52 Site1e_S91_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 921K Apr 22 17:10 Site1e_S91_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 1.6M Apr 22 16:52 Site1e_S91_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:52 Site1e_S91_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 930K Apr 22 17:10 Site1e_S91_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 1.7M Apr 22 16:52 Site1e_S91_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:52 Site1e_S91_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:53 Site1f_S92_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:53 Site1f_S92_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 16:53 Site1f_S92_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 904K Apr 22 17:10 Site1f_S92_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:53 Site1f_S92_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:53 Site1f_S92_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 918K Apr 22 17:10 Site1f_S92_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 16:53 Site1f_S92_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:53 Site1f_S92_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:53 Site1g_S93_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:53 Site1g_S93_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:53 Site1g_S93_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 914K Apr 22 17:10 Site1g_S93_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.7M Apr 22 16:53 Site1g_S93_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:53 Site1g_S93_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 921K Apr 22 17:10 Site1g_S93_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:53 Site1g_S93_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:53 Site1g_S93_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:54 Site1h_S94_L001-fastp.stderr -rw-rw-r-- 1 sam sam 486K Apr 22 16:54 Site1h_S94_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 172K Apr 22 16:54 Site1h_S94_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 916K Apr 22 17:10 Site1h_S94_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 3.5M Apr 22 16:54 Site1h_S94_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:54 Site1h_S94_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 932K Apr 22 17:10 Site1h_S94_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 3.8M Apr 22 16:54 Site1h_S94_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:54 Site1h_S94_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:54 Site1J_S99_L001-fastp.stderr -rw-rw-r-- 1 sam sam 482K Apr 22 16:54 Site1J_S99_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 169K Apr 22 16:54 Site1J_S99_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 909K Apr 22 17:10 Site1J_S99_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 1.1M Apr 22 16:54 Site1J_S99_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:54 Site1J_S99_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 930K Apr 22 17:10 Site1J_S99_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 851K Apr 22 16:54 Site1J_S99_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 16:54 Site1J_S99_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:54 Site1k_S100_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 16:54 Site1k_S100_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 16:54 Site1k_S100_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 919K Apr 22 17:10 Site1k_S100_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 7.1M Apr 22 16:54 Site1k_S100_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1k_S100_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 929K Apr 22 17:10 Site1k_S100_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 7.0M Apr 22 16:54 Site1k_S100_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1k_S100_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:54 Site1L_S101_L001-fastp.stderr -rw-rw-r-- 1 sam sam 486K Apr 22 16:54 Site1L_S101_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 171K Apr 22 16:54 Site1L_S101_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 921K Apr 22 17:10 Site1L_S101_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 2.6M Apr 22 16:54 Site1L_S101_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1L_S101_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 931K Apr 22 17:10 Site1L_S101_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 3.0M Apr 22 16:54 Site1L_S101_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1L_S101_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:54 Site1m_S102_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:54 Site1m_S102_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:54 Site1m_S102_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 916K Apr 22 17:10 Site1m_S102_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.9M Apr 22 16:54 Site1m_S102_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1m_S102_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 929K Apr 22 17:10 Site1m_S102_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:54 Site1m_S102_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:54 Site1m_S102_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:55 Site1n_S103_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:55 Site1n_S103_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 16:55 Site1n_S103_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 919K Apr 22 17:10 Site1n_S103_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 14M Apr 22 16:55 Site1n_S103_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:55 Site1n_S103_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 906K Apr 22 17:10 Site1n_S103_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 15M Apr 22 16:55 Site1n_S103_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:55 Site1n_S103_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:56 Site1o_S104_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:56 Site1o_S104_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:56 Site1o_S104_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 917K Apr 22 17:10 Site1o_S104_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 16:56 Site1o_S104_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:56 Site1o_S104_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 924K Apr 22 17:10 Site1o_S104_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 16:56 Site1o_S104_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:56 Site1o_S104_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.1K Apr 22 16:56 Site1p_S105_L001-fastp.stderr -rw-rw-r-- 1 sam sam 491K Apr 22 16:56 Site1p_S105_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 177K Apr 22 16:56 Site1p_S105_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 916K Apr 22 17:10 Site1p_S105_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 55M Apr 22 16:56 Site1p_S105_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:56 Site1p_S105_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 901K Apr 22 17:10 Site1p_S105_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 56M Apr 22 16:56 Site1p_S105_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:56 Site1p_S105_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:57 Site1q_S106_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:57 Site1q_S106_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 16:57 Site1q_S106_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 931K Apr 22 17:10 Site1q_S106_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 5.8M Apr 22 16:57 Site1q_S106_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:57 Site1q_S106_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 935K Apr 22 17:10 Site1q_S106_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 6.2M Apr 22 16:57 Site1q_S106_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:57 Site1q_S106_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:57 Site1r_S111_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:57 Site1r_S111_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:57 Site1r_S111_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 921K Apr 22 17:10 Site1r_S111_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 8.5M Apr 22 16:57 Site1r_S111_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:57 Site1r_S111_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 942K Apr 22 17:10 Site1r_S111_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 9.6M Apr 22 16:57 Site1r_S111_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:57 Site1r_S111_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:58 Site1s_S112_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 16:58 Site1s_S112_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:58 Site1s_S112_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 915K Apr 22 17:10 Site1s_S112_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 16:58 Site1s_S112_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1s_S112_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 929K Apr 22 17:10 Site1s_S112_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 16:58 Site1s_S112_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1s_S112_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:58 Site1t_S113_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:58 Site1t_S113_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:58 Site1t_S113_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 913K Apr 22 17:10 Site1t_S113_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 16:58 Site1t_S113_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1t_S113_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 900K Apr 22 17:10 Site1t_S113_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 16:58 Site1t_S113_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1t_S113_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:58 Site1U_S114_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 16:58 Site1U_S114_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 171K Apr 22 16:58 Site1U_S114_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 889K Apr 22 17:10 Site1U_S114_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 3.2M Apr 22 16:58 Site1U_S114_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1U_S114_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 916K Apr 22 17:10 Site1U_S114_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 3.6M Apr 22 16:58 Site1U_S114_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:58 Site1U_S114_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:59 Site1v_S117_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:59 Site1v_S117_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:59 Site1v_S117_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 915K Apr 22 17:10 Site1v_S117_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.0M Apr 22 16:59 Site1v_S117_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:59 Site1v_S117_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 910K Apr 22 17:10 Site1v_S117_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 9.9M Apr 22 16:59 Site1v_S117_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:59 Site1v_S117_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 16:59 Site1w_S118_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 16:59 Site1w_S118_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 16:59 Site1w_S118_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 922K Apr 22 17:10 Site1w_S118_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.6M Apr 22 16:59 Site1w_S118_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:59 Site1w_S118_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 937K Apr 22 17:10 Site1w_S118_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 16:59 Site1w_S118_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 16:59 Site1w_S118_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:00 Site1y_S120_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:00 Site1y_S120_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:00 Site1y_S120_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 930K Apr 22 17:10 Site1y_S120_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 8.3M Apr 22 17:00 Site1y_S120_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:00 Site1y_S120_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 943K Apr 22 17:10 Site1y_S120_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 9.3M Apr 22 17:00 Site1y_S120_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:00 Site1y_S120_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:00 Site1z_S129_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:00 Site1z_S129_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:00 Site1z_S129_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 928K Apr 22 17:10 Site1z_S129_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 6.6M Apr 22 17:00 Site1z_S129_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:00 Site1z_S129_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 940K Apr 22 17:10 Site1z_S129_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 7.3M Apr 22 17:00 Site1z_S129_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:00 Site1z_S129_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:01 Site5aa_S132_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 17:01 Site5aa_S132_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 17:01 Site5aa_S132_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 927K Apr 22 17:11 Site5aa_S132_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 17M Apr 22 17:01 Site5aa_S132_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:01 Site5aa_S132_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 925K Apr 22 17:11 Site5aa_S132_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 18M Apr 22 17:01 Site5aa_S132_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:01 Site5aa_S132_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:01 Site5a_S87_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:01 Site5a_S87_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:01 Site5a_S87_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 932K Apr 22 17:10 Site5a_S87_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 5.5M Apr 22 17:01 Site5a_S87_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:01 Site5a_S87_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 942K Apr 22 17:10 Site5a_S87_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 6.5M Apr 22 17:01 Site5a_S87_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:01 Site5a_S87_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:02 Site5bb_S133_L001-fastp.stderr -rw-rw-r-- 1 sam sam 491K Apr 22 17:02 Site5bb_S133_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 176K Apr 22 17:02 Site5bb_S133_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 927K Apr 22 17:11 Site5bb_S133_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 21M Apr 22 17:02 Site5bb_S133_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:02 Site5bb_S133_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 929K Apr 22 17:11 Site5bb_S133_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 23M Apr 22 17:02 Site5bb_S133_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:02 Site5bb_S133_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:02 Site5b_S88_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 17:02 Site5b_S88_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:02 Site5b_S88_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 911K Apr 22 17:11 Site5b_S88_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 8.7M Apr 22 17:02 Site5b_S88_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:02 Site5b_S88_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 916K Apr 22 17:11 Site5b_S88_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 17:02 Site5b_S88_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:02 Site5b_S88_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.1K Apr 22 17:03 Site5cc_S134_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 17:03 Site5cc_S134_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 17:03 Site5cc_S134_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 912K Apr 22 17:11 Site5cc_S134_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 22M Apr 22 17:03 Site5cc_S134_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:03 Site5cc_S134_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 911K Apr 22 17:11 Site5cc_S134_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 27M Apr 22 17:03 Site5cc_S134_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:03 Site5cc_S134_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:03 Site5c_S89_L001-fastp.stderr -rw-rw-r-- 1 sam sam 486K Apr 22 17:03 Site5c_S89_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 172K Apr 22 17:03 Site5c_S89_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 927K Apr 22 17:11 Site5c_S89_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 3.7M Apr 22 17:03 Site5c_S89_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:03 Site5c_S89_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 930K Apr 22 17:11 Site5c_S89_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 3.9M Apr 22 17:03 Site5c_S89_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:03 Site5c_S89_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:03 Site5ee_S136_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 17:03 Site5ee_S136_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 17:03 Site5ee_S136_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 920K Apr 22 17:11 Site5ee_S136_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 14M Apr 22 17:03 Site5ee_S136_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:03 Site5ee_S136_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 916K Apr 22 17:11 Site5ee_S136_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 16M Apr 22 17:03 Site5ee_S136_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:03 Site5ee_S136_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:04 Site5e_S95_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 17:04 Site5e_S95_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 17:04 Site5e_S95_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 911K Apr 22 17:11 Site5e_S95_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 17:04 Site5e_S95_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:04 Site5e_S95_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 905K Apr 22 17:11 Site5e_S95_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 17:04 Site5e_S95_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:04 Site5e_S95_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.1K Apr 22 17:04 Site5ff_S137_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 17:04 Site5ff_S137_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 176K Apr 22 17:04 Site5ff_S137_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 905K Apr 22 17:11 Site5ff_S137_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 25M Apr 22 17:04 Site5ff_S137_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:04 Site5ff_S137_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 905K Apr 22 17:11 Site5ff_S137_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 28M Apr 22 17:04 Site5ff_S137_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 68 Apr 22 17:04 Site5ff_S137_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:04 Site5f_S96_L001-fastp.stderr -rw-rw-r-- 1 sam sam 482K Apr 22 17:04 Site5f_S96_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 168K Apr 22 17:04 Site5f_S96_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 913K Apr 22 17:11 Site5f_S96_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 672K Apr 22 17:04 Site5f_S96_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:04 Site5f_S96_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 910K Apr 22 17:11 Site5f_S96_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 573K Apr 22 17:04 Site5f_S96_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:04 Site5f_S96_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:05 Site5g_S97_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 17:05 Site5g_S97_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:05 Site5g_S97_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 911K Apr 22 17:11 Site5g_S97_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 8.8M Apr 22 17:05 Site5g_S97_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:05 Site5g_S97_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 940K Apr 22 17:11 Site5g_S97_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 9.8M Apr 22 17:05 Site5g_S97_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:05 Site5g_S97_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:05 Site5h_S98_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 17:05 Site5h_S98_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 175K Apr 22 17:05 Site5h_S98_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 912K Apr 22 17:11 Site5h_S98_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 17:05 Site5h_S98_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:05 Site5h_S98_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 904K Apr 22 17:11 Site5h_S98_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 13M Apr 22 17:05 Site5h_S98_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 66 Apr 22 17:05 Site5h_S98_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:05 Site5J_S107_L001-fastp.stderr -rw-rw-r-- 1 sam sam 456K Apr 22 17:05 Site5J_S107_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 136K Apr 22 17:05 Site5J_S107_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 951K Apr 22 17:11 Site5J_S107_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 3.1K Apr 22 17:05 Site5J_S107_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:05 Site5J_S107_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 956K Apr 22 17:11 Site5J_S107_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 3.2K Apr 22 17:05 Site5J_S107_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:05 Site5J_S107_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:05 Site5k_S108_L001-fastp.stderr -rw-rw-r-- 1 sam sam 486K Apr 22 17:05 Site5k_S108_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 172K Apr 22 17:05 Site5k_S108_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 919K Apr 22 17:11 Site5k_S108_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 3.4M Apr 22 17:05 Site5k_S108_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:05 Site5k_S108_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 918K Apr 22 17:11 Site5k_S108_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 4.2M Apr 22 17:05 Site5k_S108_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:05 Site5k_S108_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:06 Site5L_S109_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:06 Site5L_S109_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:06 Site5L_S109_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 913K Apr 22 17:11 Site5L_S109_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 17:06 Site5L_S109_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5L_S109_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 918K Apr 22 17:11 Site5L_S109_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 12M Apr 22 17:06 Site5L_S109_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5L_S109_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:06 Site5m_S110_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:06 Site5m_S110_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 17:06 Site5m_S110_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 914K Apr 22 17:11 Site5m_S110_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 6.1M Apr 22 17:06 Site5m_S110_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5m_S110_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 927K Apr 22 17:11 Site5m_S110_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 7.0M Apr 22 17:06 Site5m_S110_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5m_S110_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:06 Site5n_S115_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 17:06 Site5n_S115_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 17:06 Site5n_S115_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 925K Apr 22 17:11 Site5n_S115_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 6.1M Apr 22 17:06 Site5n_S115_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5n_S115_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 936K Apr 22 17:11 Site5n_S115_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 6.6M Apr 22 17:06 Site5n_S115_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:06 Site5n_S115_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:07 Site5o_S116_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 17:07 Site5o_S116_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 17:07 Site5o_S116_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 932K Apr 22 17:11 Site5o_S116_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 5.8M Apr 22 17:07 Site5o_S116_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:07 Site5o_S116_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 939K Apr 22 17:11 Site5o_S116_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 6.4M Apr 22 17:07 Site5o_S116_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:07 Site5o_S116_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:07 Site5p_S121_L001-fastp.stderr -rw-rw-r-- 1 sam sam 488K Apr 22 17:07 Site5p_S121_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:07 Site5p_S121_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 921K Apr 22 17:11 Site5p_S121_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 7.7M Apr 22 17:07 Site5p_S121_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:07 Site5p_S121_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 924K Apr 22 17:11 Site5p_S121_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 8.8M Apr 22 17:07 Site5p_S121_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:07 Site5p_S121_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:08 Site5q_S122_L001-fastp.stderr -rw-rw-r-- 1 sam sam 490K Apr 22 17:08 Site5q_S122_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:08 Site5q_S122_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 901K Apr 22 17:11 Site5q_S122_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 15M Apr 22 17:08 Site5q_S122_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5q_S122_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 916K Apr 22 17:11 Site5q_S122_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 16M Apr 22 17:08 Site5q_S122_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5q_S122_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:08 Site5r_S123_L001-fastp.stderr -rw-rw-r-- 1 sam sam 489K Apr 22 17:08 Site5r_S123_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 174K Apr 22 17:08 Site5r_S123_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 927K Apr 22 17:11 Site5r_S123_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 9.3M Apr 22 17:08 Site5r_S123_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5r_S123_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 930K Apr 22 17:11 Site5r_S123_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 11M Apr 22 17:08 Site5r_S123_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5r_S123_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:08 Site5s_S124_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 17:08 Site5s_S124_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 17:08 Site5s_S124_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 906K Apr 22 17:11 Site5s_S124_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 7.1M Apr 22 17:08 Site5s_S124_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5s_S124_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 916K Apr 22 17:11 Site5s_S124_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 8.4M Apr 22 17:08 Site5s_S124_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:08 Site5s_S124_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:09 Site5u_S126_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 17:09 Site5u_S126_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 173K Apr 22 17:09 Site5u_S126_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 922K Apr 22 17:11 Site5u_S126_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 4.8M Apr 22 17:09 Site5u_S126_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5u_S126_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 926K Apr 22 17:11 Site5u_S126_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 5.4M Apr 22 17:09 Site5u_S126_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5u_S126_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:09 Site5v_S127_L001-fastp.stderr -rw-rw-r-- 1 sam sam 487K Apr 22 17:09 Site5v_S127_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 172K Apr 22 17:09 Site5v_S127_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 940K Apr 22 17:11 Site5v_S127_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 4.2M Apr 22 17:09 Site5v_S127_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5v_S127_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 946K Apr 22 17:11 Site5v_S127_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 4.6M Apr 22 17:09 Site5v_S127_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5v_S127_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:09 Site5w_S128_L001-fastp.stderr -rw-rw-r-- 1 sam sam 437K Apr 22 17:09 Site5w_S128_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 120K Apr 22 17:09 Site5w_S128_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 833K Apr 22 17:11 Site5w_S128_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 1.2K Apr 22 17:09 Site5w_S128_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5w_S128_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 857K Apr 22 17:11 Site5w_S128_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 1.3K Apr 22 17:09 Site5w_S128_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5w_S128_L001_R2_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 2.0K Apr 22 17:09 Site5z_S131_L001-fastp.stderr -rw-rw-r-- 1 sam sam 492K Apr 22 17:09 Site5z_S131_L001.fastp-trim.report.html -rw-rw-r-- 1 sam sam 177K Apr 22 17:09 Site5z_S131_L001.fastp-trim.report.json -rw-rw-r-- 1 sam sam 894K Apr 22 17:11 Site5z_S131_L001_R1_001_fastqc.html -rw-rw-r-- 1 sam sam 33M Apr 22 17:09 Site5z_S131_L001_R1_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:09 Site5z_S131_L001_R1_001.fastq.gz.md5 -rw-rw-r-- 1 sam sam 909K Apr 22 17:11 Site5z_S131_L001_R2_001_fastqc.html -rw-rw-r-- 1 sam sam 37M Apr 22 17:09 Site5z_S131_L001_R2_001.fastq.gz -rw-rw-r-- 1 sam sam 67 Apr 22 17:10 Site5z_S131_L001_R2_001.fastq.gz.md5
Chen, Shifu. 2023. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” *iMeta* 2 (2). .
Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” *Bioinformatics* 32 (19): 3047–48. .