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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
116 stars 33 forks source link

Add support for sequencing coverage esimates with nonpareil #384

Closed jfy133 closed 9 months ago

jfy133 commented 11 months ago

Description of feature

Main module here: https://github.com/nf-core/modules/pull/3885

Might be nice to also make a MultiQC module for rendering curves.

Important: requires uncompressing FASTQ files for input! will need to give big warnings about disk space on this.

jfy133 commented 10 months ago

Maybe should update the module to conditionally unzip within it, rather than expected it outside

Midnighter commented 10 months ago

I was thinking, it would be awesome to have a QC step that shows an overview of where classified reads map on the identified reference genomes. Can nonpareil generally do that or does it only deliver estimates on how much coverage was achieved?

jfy133 commented 10 months ago

No, it purely aligns reads to themselves to check for redundancy essentially.

I'm not really sure there is a tool that does what you're asking for at a metagenomic level...

jfy133 commented 9 months ago

Done in in the pr that GitHub mobile is not finding stm