This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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
• 2,974 views • link
updated by LauferVA LauferVA • written by Bogdan Bogdan

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

• 0 views • link
written by LauferVA LauferVA

The ENCODE pipelines are also runnable on the Truwl platform

• 0 views • link
written by Jeremy Leipzig Jeremy Leipzig

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.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this