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CLI for JAWS users

metagenome/metatranscriptome assembly and reporting code

The IMG Annotation Pipeline (IMGAP) is used for structural and functional annotation of prokaryotic genomes, metagenomes and metatranscriptomes submitted to the DOE Joint Genome Institute's IMG system.

Code supporting genome assembly and analysis of small Eukaryotes, fungi, algae, organelles.

These are WDL examples that are used by the JAWS tutorials in the jaws-docs.readthedocs.io.

sblast portion of the IMG isolates pipeline, reworked to use the JAWS infrastructure

Recreates the phyloDist steps of the isolates pipeline using the JAWS infrastructure, with a few QOL improvements as well.

The inhomo3 portion of the Isolate Pipeline, but recreating using WDL infrastructure and Docker containers.

Creation of a wdl for the horizontal transfer portion (horTransfer2) of the isolates pipeline.