bioinformatics pipelines on GCP or AWS

Question

[Bogdan]

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

Answer 1

[LauferVA]

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

[Jeremy Leipzig]

The ENCODE pipelines are also runnable on the Truwl platform

Answer 2

[GenoMax]

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.

Answer 3

[Alex Reynolds]

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/