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bioinformatics pipelines on GCP or AWS

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
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updated by LauferVA 497 • | written by Bogdan 144

3 answers

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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written by LauferVA 497

The ENCODE pipelines are also runnable on the Truwl platform

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written by Jeremy Leipzig 2.3K

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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written by GenoMax 16K

Genomics Workflows on AWS: https://docs.opendata.aws/genomics-workflows/

Some information here on GATK on AWS: https://aws.amazon.com/blogs/industries/running-gatk-workflows-on-aws-a-user-friendly-solution/

These resources might be generally useful, as well: https://aws.amazon.com/government-education/research-and-technical-computing/research-seminar-series/

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written by Alex Reynolds 3.6K

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