Good pratice for clinical NGS data pipelines
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4.7 years ago
vmicrobio ▴ 290

Hello everyone!

I have a very general question. Does anybody have advices, guidelines, papers, softwares about good practice for clinical NGS data pipelines? My aim is to set up a quality process for my lab using a home made build pipeline or something already existing.

What I have in mind (but definitely not sufficient) : analysis and control (log files during all the process) of data generated from sequencing and post-sequencing analysis (vcf, contigs files...) and also generation of a clear and synthetic report

I found these valued articles :

-Good laboratory practice for clinical next-generation sequencing informatics pipelines (Nat Biotechnol. 2015)

-Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests (J Pathol Transl Med. 2017)

and also some tracks with samtools (flagstat, depth,...) and bedtools (coverageBed, intersectBed,...)

Thanks for your advices!

good practices clinical NGS tools • 1.5k views
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4.7 years ago
chen ★ 2.4k

Let me show u an example:
https://github.com/OpenGene/ctdna-pipeline
A simplified pipeline for ctDNA sequencing data analysis

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Hi Chen, Thank you for your answer, your pipeline is cool, very clear and well documented but except for read filtering I don't see any controls, graphs or reports to validate quality of the data and also analysis process

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