Remove Mitochondrial Reads from Genome reads

Question

[hpalk42]

Hello, I am assembling a very large and repetitive genome, and I was advised to remove the mtDNA reads to make the assembly process run smoother. We are hoping that removing the mt reads will lower the file sizes some which would help with memory requirements. I have assembled the mitochondrial genome, but what software is recommended to take mitochondrial reads out of the genomic sequencing reads? I have two paired-end, trimmed fastq files that I would like to separate the mitochondrial reads from. Any recommendations? Thank you so much!

Answer 1

[GenoMax]

You can use bbsplit.sh from BBMap suite to separate the reads belonging to MT genome.

See: BBSplit syntax for generating builds for the reference genome and how to call different builds. reads in outu1 and outu2 files will be free of MT data.