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nf-core / exoseq

Please consider using/contributing to https://github.com/nf-core/sarek
http://nf-co.re
MIT License
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Difference of pipelines #40

Open kokyriakidis opened 5 years ago

kokyriakidis commented 5 years ago

What is the difference between this and Sarek pipeline?

maxulysse commented 5 years ago

Hi,

Sorry, I did not notice this question before, so I'm only replying now.

Sarek was at the beginning designed to analyse tumor/normal pairs (and additional relapses), but we realised that it could work with just normal samples as well. Sarek was at the beginning a WGS analysis project, and we're still adding possibilities for analysing WES and targeted sequencing.

This nf-core/exoseq pipeline was designed since the beginning to analyse Exome data, so it's definitively less complicated, and it obviously doesn't work on WGS.

I also think that the development is on hold at the moment.

apeltzer commented 5 years ago

That pretty much sums it up for the moment 👍

Note that there were some thoughts to make this work at least for exomes, but Sarek covers much of this use case so we put a hold on it...