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