bioinformatics pipelines on GCP or AWS
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11 months ago
Bogdan ★ 1.3k

Dear all,

would you please let me know if there are bioinformatics pipelines (RNA-seq, ChIP-seq, ATAC-seq, etc) already available on GCP or AWS ?

it would be a good resource in order to each the students.

thanks,

Bogdan

RNA-seq google ChIP-seq cloud • 884 views
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6 months ago
Vincent Laufer ★ 2.2k

Hello Bogdan,

I think we would be remiss if we didn't mention the ENCODE pipelines, which are:

  1. Open-sourced.
  2. Made for use with Docker and Singularity.
  3. Well-maintained.

Please see: https://github.com/ENCODE-DCC

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The ENCODE pipelines are also runnable on the Truwl platform

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11 months ago
GenoMax 119k

There are core-pipelines available in NextFlow (https://nf-co.re/pipelines ) and Snakemake (https://github.com/snakemake-workflows ). They can be easily run on any cloud infrastructure.

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