Degenerate primer/adaptor removal tool for Galaxy?

Question

[shortridge.15]

Hi there,

I am working on a next generation sequencing dataset and can't seem to find a tool on Galaxy despite extensive searching that can handle degenerate primers. I would like to remove them from my dataset as part of the cleanup steps. Does anyone know of a tool that can do this? P.S. I program in Python (but also somewhat in Perl and R) so writing a script is a possibility, but I am running Galaxy to help with sharing data and analyses with collaborators.

Thanks so much!

Meg

[Biomonika (Noolean)]

You may have more luck at Galaxy biostars: https://biostar.usegalaxy.org/

Answer 1

[shortridge.15]

If anyone finds that they need this tool, it is now available on the Galaxy ToolShed as "Cut degenerate primers from dataset."

Here is the link: https://toolshed.g2.bx.psu.edu/repository?repository_id=25ad6aeb8b2d047f

It uses a simple Python script.

Cheers,
Meg