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Jetstream Resources

Collection of tools and scripts what can be used to summarize or build required annotation files for a JetStream workflow.

What is JetStream?

JetStream is the pipeline management system used at TGen. In a simple form it can be used to create analysis workflows based on user defined tasks that are linked by a series of directives. In the advanced form, like the provided workflows, project specific JSON files are integrated with template files to render a DAG that is then executed by a JetStream runner on a local or distributed computing environment. For more details see the JetStream repository (https://github.com/tgen/jetstream)

JetStream Workflows

Multiple workflows exist to facilitate different analysis projects

Phoenix (https://github.com/tgen/phoenix)

  • Human analyis pipeline built around the GRCh38 reference genome and Ensembl version 98 gene models
    • Ensembl v98 is equivalent to Gencode v32
  • Scripts used to build all required annotation files can be found in the "phoenix" directory

Suncity (https://github.com/tgen/suncity)

  • Developed for legacy project support
  • Human analysis pipeline built around GRCh37, using the 1000 genomes hs37d5 reference, and ensembl GRCh37 archive gene models

Coyote (https://github.com/tgen/coyote)

  • Dog analysis pipeline built around CanFam3.1, using ensembl version 98 gene models

CactusMouse (https://github.com/tgen/cactusMouse)

  • Mouse analysis pipeline built around mm10, using ..

Other Provided Tools and Resources

Utility Files

  • Files required for scripts in this repository

Utility Scripts

  • Fully parameterized scripts that can be used to create common outputs
    • annotation databases
    • alignment indexes
    • compile tools (used in testing only, production install by HPC)
    • transcriptome fasta