Assembles paired-end reads with metaSPAdes, identifies candidate plasmids/chromosomes/viruses with PlasMAAG, annotates plasmids with MOB-typer and Plasmer, and maps each sample’s assembly contigs back to the discovered plasmid catalog with mmseqs2.
This is a companion discussion topic for the original entry at github.com/marcoteix/wdl-workflows/PlasMAAG