/gannet/Atumefaciens/20190401_metagenomics_pgen_anvio

Metagenomics analysis of P.generosa (geoduck) water filter samples using Anvi'o metagenomics pipeline.

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FILES

- 20190401_metagenomics_pgen_anvio.sh: SBATCH script for Mox job.

- contigs.db: Anvi'o contigs database file.

- fastq.list.txt: List of input FastQ files used for analysis.

- megahit_assembly.renamed.fa: MEGAHIT assembly FastA (from 20190102) with descriptor lines renamed to be compliant.

- megahit_assembly.renamed.fa.fai: FastA index file.

- megahit_assembly.renamed.txt: Text file mapping of new FastA descriptors to originals.

- *.aln.sam.gz: Gzipped SAM; BBmap output of read alignments to each individual sample.

- *.bam: BAM files created for each sample by Anvi'o "anvi-init-bam" command. Essentially, just a sorted BAM file.

- *.bam-ANVIO_PROFILE: Anvi'o profile database for each sample.

- *.bam.bai: BAM file index for each sample.

- *.RAW.bam: BAM file generated from each unzipped SAM file through samtools. Un-sorted.

- *.RAW.sam: SAM file generated from each gzipped SAM file by gunzip.

- *.renamed.fa: Individual FastA assemblies with descriptor lines renamed to be compliant with "anvi-script-reformat-fasta".

- *.renamed.fa.fai: FastA index file.

- *.renamed.txt: Text file mapping of new FastA descriptors to originals.

- ref: Reference directory created and used by BBmap for alignments.

- SAMPLES-MERGED: Anvi'o directory containing two databases of all merged data.

- slurm-739066.out: SLURM output file (i.e. stderr/stdout).

- system_path.log: List of Sam's Mox system $PATH contents.

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Notebook:

https://robertslab.github.io/sams-notebook/2019/04/01/Metagenomics-Taxonomic-Diversity-Comparisons-from-Geoduck-Water-with-Anvio-on-Mox.html