Tools for classifying human and mouse reads for WGS data

Question

[sgujja]

Hello, I am looking for suggestions on using tools for classifying human and mouse reads for PDX WGS data. Xenome for RNA-Seq works well.Any input on tools designed for DNA-Seq? Thanks

Answer 1

[Ron]

https://sourceforge.net/projects/bbmap/

BBSplit will map the reads simultaneously to multiple references, and output in multiple files, one per reference.

Refer to this post: Tool to separate human and mouse rna seq reads