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Python script to process NGS data

I want to develop a script in python that automates the conversion of FASTQ to CRAM files (BWA-MEM2, GEM, etc), to BAM files (SAMTools, etc) and to Variants (BCF Tools, etc). After that, I want to develop a web application.

Is it possible?

python
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updated by Ram Ram • written by anasjamshed anasjamshed

FYI, there's a dedicated workflow managers for this approach, for example snakemake, nextflow (with tower as UI), CWL.

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written by Carambakaracho Carambakaracho

1 answer

.... yes it is possible; the nuances of this possibility is the subject of tens of thousands of articles, webpages, software packages, etc. I hope that helps.

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written by LauferVA LauferVA

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