genomic-medicine-sweden / jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

https://jasen.readthedocs.io/en/latest/

GNU General Public License v3.0

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Add read downsampling as a pre processing step #364

Closed mhkc closed 2 weeks ago

mhkc commented 2 weeks ago

Description

This PR adds an optional preprocessing step for downsampling the number of reads to a given target. This because extremely high sequencing depth can negatively affect the de-novo assembly quality.

Primary function of PR

[ ] Hotfix
[x] Minor functionality improvement
[ ] Major functionality improvement / New type of analysis
[ ] Backward-breaking functionality

Sign-offs

[ ] Code reviewed by @octocat
[ ] Code tested by @octocat