removing chloroplast sequence from FASTQ files

Question

[Ric]

Hi, I have paired-end WGS FASTQ files and chloroplast genome. How is it possible to remove chloroplast sequences from the FASTQ files?

Thank you in advance.

Mic

Answer 1

[GenoMax]

Use BBSplit from BBMap to bin the reads (chloro and non-chloro) as noted here: BBSplit syntax for generating builds for the reference genome and how to call different builds.