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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.
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De-novo transcriptome assembly from RNA-seq data using Trinity
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Synthetic biology team's WDL based pipeline for validation of PacBio sequence.
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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.
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Python modules focused on pre and post processing around WDL workflows that are executed via JAWS.
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Recreates the phyloDist steps of the isolates pipeline using the JAWS infrastructure, with a few QOL improvements as well.
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sblast portion of the IMG isolates pipeline, reworked to use the JAWS infrastructure
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The inhomo3 portion of the Isolate Pipeline, but recreating using WDL infrastructure and Docker containers.
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Creation of a wdl for the horizontal transfer portion (horTransfer2) of the isolates pipeline.
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Code supporting genome assembly and analysis of small Eukaryotes, fungi, algae, organelles.
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