search

dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
278 stars 99 forks source link

MAXKMERLENGTH = 255 #55

Closed joseboas closed 2 years ago

joseboas commented 2 years ago

I want to change the MAXKMERLENGTH to 255. I downloaded the conda version.

dzerbino commented 2 years ago

Hello Jose,

The change the MAXKMERLENGTH you need to download and recompile the source code as explained in the Manual.

I don't know if that is possible with conda and may require you downloading the Git repository itself: https://github.com/dzerbino/velvet/archive/refs/heads/master.zip

Best regards,

Daniel

joseboas commented 2 years ago

OK. Thanks for the feedback.

bernt-matthias commented 2 years ago

The velvet version provided by bioconda currently sets the value to 191: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/velvet/build.sh

If you like to use 255 you may open a PR to the bioconda recipes repo.