https://github.com/broadinstitute/long-read-pipelines

Long read production pipelines
https://github.com/broadinstitute/long-read-pipelines

de-novo-assembly long-reads pipelines variant-calling wdl

Last synced: about 1 year ago
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Long read production pipelines

• Host: GitHub
• URL: https://github.com/broadinstitute/long-read-pipelines
• Owner: broadinstitute
• License: bsd-3-clause
• Created: 2019-05-14T16:12:33.000Z (about 7 years ago)
• Default Branch: main
• Last Pushed: 2024-12-02T16:38:29.000Z (over 1 year ago)
• Last Synced: 2024-12-04T19:31:19.058Z (over 1 year ago)
• Topics: de-novo-assembly, long-reads, pipelines, variant-calling, wdl
• Language: Jupyter Notebook
• Homepage: https://broadinstitute.github.io/long-read-pipelines/
• Size: 215 MB
• Stars: 142
• Watchers: 16
• Forks: 24
• Open Issues: 121
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# Long read pipelines

This repository contains pipelines for processing of long read data from PacBio and/or Oxford Nanopore platforms.  The pipelines are written in [WDL 1.0](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#introduction) intended for use with Google Cloud Platform via the scientific workflow engine, [Cromwell](https://github.com/broadinstitute/cromwell).  Processing is designed to be reasonably consistent between both long read platforms, and use platform-specific options or tasks where necessary.

High level workflows can be found in the wdl/ directory.

**Documentation**: Documentation for each workflow can be found at the repository [site](https://broadinstitute.github.io/long-read-pipelines/).

**External Contributors**: Please see the [Contributing Guidelines](https://broadinstitute.github.io/long-read-pipelines/development_guide/#contributing-guidelines) for information on how to contribute to the repository.