Sam’s Notebook: Metagenomics – Geoduck Water Sample Assembly Comparisons with MetaQuast

As part of addressing this GitHub Issue on assessing taxonomic diversity in our metagenomics samples, I decided to compare the individual sample assemblies I made on 20190327 using Megahit and the assemblies that Emma made. Emma utilized NGless on her cluster in Genome Sciences with the following scripts:

  #!/bin/bash #$ -cwd #$ -S /bin/bash #$ -o ./output #$ -e ./output #$ -l mfree=3G #$ -pe serial 16 #$ -R y # Send email when job starts, ends or runs into an error #$ -m beas #$ -M emmats@uw.edu #cause a failing process to trigger a job failure to make errors easier to catch set -eo pipefail #Initialize and load modules . /etc/profile.d/modules.sh module purge module load modules{,-{init,gs/prod}} ngless/0.10.0 #Script ngless \ /net/nunn/vol1/emmats/sequencing/geo_metaG/ngl.singleLibs \ --trace \ --keep-temporary-files \ -j $NSLOTS \ -t /data/scratch/ssd