Explore projects

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

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

A gene homology search service

A sequence ID mapping service

A set of docker images that can be useful for the development and testing of WDL pipelines.

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.

CLI for JAWS users

metagenome/metatranscriptome assembly and reporting code

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

Synbio team miseq short read validation.

IMG annotation pipeline. It is the central repo for NMDC, IMG and the Advanced Analysis group. The following WDL was derived (and maintained by) Marcel Huntemann's pipeline.

An attempt to create a series of wrapper scripts that will submit to jaws, continually check to see if the run has succeeded, and then gatherFiles afterwards.

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

De-novo transcriptome assembly from RNA-seq data using Trinity

update dockerhub image location