SergejN

that would be extremely important and helpful! Vote up!

thanks! this is very helpful and will save me a lot of time :)

> You can run the mapper as: > > ``` > winnowmap -W repetitive_k15.txt -ax map-ont ref.fa ont1.fq.gz ont2.fq.gz ont3.fq.gz ... > ``` > > Will this resolve your issue?...

Yes, sure. This will also work, unless you have to specify so many files that the command line becomes too long (2MB on my system, so quite a few file...