search

hoelzer / mgnify-lr

Evaluation of long-read support for the MGnify pipeline
GNU General Public License v3.0
6 stars 5 forks source link

short-read decontamination with minimap2 removes a lot #31

Closed hoelzer closed 4 years ago

hoelzer commented 4 years ago

Compare short-read decontamination with

for example for H52 MiSeq data cleanup against phiX.

hoelzer commented 4 years ago

BBDuk might be also interesting: https://yiweiniu.github.io/blog/2018/07/Remove-Contamination-of-Pokaryotic-Organisms-in-Reads/

hoelzer commented 4 years ago

implemented bbduk as the default