Replace NanoFilt and Porechop with Chopper

Question

Replace NanoFilt and Porechop with Chopper

Closed this issue 9 months ago · 3 comments

ImagoXV commented 9 months ago

conda install -c bioconda chopper

The problem is that I still need to install conda in my dockerfile

Answer 1 · 2023-12-15T15:58:54.000Z

It's done !
I didn't use conda in the end, just the archive. Works perfectly

Answer 2 · 2024-01-24T10:34:22.000Z

In the dev branch, script.sh still calls chop_file() and porechop. Should it be removed then?

Answer 3 · 2024-01-25T10:07:48.000Z

Yes, NanoFilt was changed for chopper for efficiency reasons. Nanofilt was not maintained anymore and chopper is its rust version
However, chopper does not implement the Porechop functionalities regarding adapter trimming