Sam’s Notebook: Metagenomics – P.generosa Water Sample Assemlby Comparisons with Quast

Continuing work on the metagenomics project, Emma shared her “co-assembly”, so I figured it would be quick and easy to compare hers with mine and get a feel for how different/similar they might be. I did a similar comparison last week where I compared each of our individual water sample assemblies. Those results showed my assemblies generated:

  • significantly larger “largest contigs” (10 – 50x larger than Emma’s)
  • larger N50 values (~2x larger than Emma’s)
  • total length in bps (~1.5x more than Emma’s)

So, I ran Quast on my computer (swoose – Ubuntu 16.04LTS) with the following input FastAs:

  python \ /home/sam/programs/quast-5.0.2/ \ --threads=20 \ --min-contig=100 \ --labels=ets,sjw \ /home/sam/data/metagenomics/P_generosa/emma_assemblies/contigs.fa \ /home/sam/data/metagenomics/P_generosa/final.contigs.fa