/gannet/Atumefaciens/20190415_metagenomics_pgen_megahit

Metagenomics assemblies using MegaHit on Mox to create two pH-specific assemblies (pH=7.1 and pH=8.2).

pH=7.1: MG3, MG6, MG7
pH=8.2: MG1, MG2, MG5

Input FastQ files were from our HiSeqX data (from 2080809), previously trimmed:

https://robertslab.github.io/sams-notebook/2018/12/11/FastQC-and-Trimming-Metagenomics-(Geoduck)-HiSeqX-Reads-from-20180809.html

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FILES

- 20190415_metagenomics_pgen_megahit.sh: SBATCH scrip to run MegaHit on Mox.

- fastq.list.pH71.txt: List of all pH=7.1 FastQ files used.

- fastq.list.pH82.txt: List of all pH=8.2 FastQ files used.

- pH71: Output directory for pH=7.1 assembly (megahit_out/pH71.contigs.fa)

- pH71.all.R1.fq.gz: Concatenated pH=7.1 R1 FastQ.

- pH71.all.R2.fq.gz: Concatenated pH=7.1 R2 FastQ.

- pH82: Output directory for pH=8.2 assembly (megahit_out/pH82.contigs.fa)

- pH82.all.R1.fq.gz: Concatenated pH=8.2 R1 FastQ.

- pH82.all.R2.fq.gz: Concatenated pH=8.2 R2 FastQ.

- slurm-753555.out: The SLURM output file (contains stderr/stdout).

- system_path.log: Text file containing list of all items in Sam's Mox system $PATH variable.


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Notebook: https://robertslab.github.io/sams-notebook/2019/04/15/Metagenome-Assemblies-P.generosa-Water-Samples-Trimmed-HiSeqX-Data-Using-Megahit-on-Mox-to-Compare-pH-Treatments.html