Question: Biopython for NGS
0
gravatar for shuksi1984
22 months ago by
shuksi198460
shuksi198460 wrote:

Can I use Biopython to automate the NGS pipeline. If yes, which Biopython library can be used to run GATK, SAMTOOLS, bwa, PICARD. ? I hope my question is clear.

sequencing snp next-gen • 902 views
ADD COMMENTlink written 22 months ago by shuksi198460
2

For automated pipelines, people use what is known as snakemake

Creating workflows with snakemake and conda

Although, I frequently use shell scripting

ADD REPLYlink written 22 months ago by lakhujanivijay5.2k

While browsing, I also came across Ruffus. How about Ruffus? Which one would be better sankemake or Ruffus? Although, both are python library but there must be some difference

ADD REPLYlink written 22 months ago by shuksi198460
1

I'd suggest snakemake. As far as I know it's more widely used.

ADD REPLYlink written 22 months ago by WouterDeCoster44k
1

Other options you could explore are NextFlow/FlowCraft

ADD REPLYlink written 22 months ago by Joe18k
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