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hoelzer / mgnify-lr

Evaluation of long-read support for the MGnify pipeline
GNU General Public License v3.0
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decontamination #6

Closed hoelzer closed 4 years ago

hoelzer commented 4 years ago

Implement a decontamination procedure before and after assembly like shown here:

https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?spaceKey=MetaGen&title=Decontamination

I think the simplest way is to use minimap2 to align the long reads as well as the contigs.

When this is working, I can suggest an update/extension of the confluence web page.

hoelzer commented 4 years ago

Implemented decontamination procedure. Remains: add a fasta sequence directly via parameter