Good pratice for clinical NGS data pipelines

Question

[vmicrobio]

Hello everyone!

I have a very general question. Does anybody have advice, guidelines, papers, software 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 advice!

Answer 1

[chen]

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

[vmicrobio]

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