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metagenome/metatranscriptome assembly and reporting code

CLI for JAWS users

RNA virus analysis toolkit, including a variety of commands and wrappers for external tools (from raw read processing to genome annotation).

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.

Synthetic biology team's WDL based pipeline for validation of PacBio sequence.

The synbioqc-pbj pipeline altered for running the qc pipeline on reference sequences that have been barcoded prior to the PacBio barcoding and adapter additions, so these must be demultiplexed prior to the qc analysis.

Synbio team miseq short read validation.

Documentation for RolyPoly