/gannet/Atumefaciens/20190102_metagenomics_geo_megahit Metagenomic assembly of Panopea generosa water samples using Megahit, run on Mox. All samples were assembled into a single large assembly. BBmap BBwrap/pileup were used to generate sequencing alignments and coverage. --- FILES - 20190102_metagenomics_geo_megahit.sh: SBATCH script to run job on Mox. - aln.sam.gz: BBmap BBwrap alignment SAM file - gzipped. See SBATCH script for commands used to generate file. - coverage.txt: BBmap pileup.sh coverage file generated from SAM file. See SBATCH script for commands used to generate file. - megahit_out: Megahit output folder. - ref: Genome reference directory created by BBmap. - slurm-553487.out: SLURM output file (i.e. stderr/stdout). - system_path.log: List of Sam's Mox system $PATH contents. --- Notebook: https://robertslab.github.io/sams-notebook/2019/01/02/Metagenome-Assembly-P.generosa-Water-Sample-HiSeqX-Data-Using-Megahit.html