removing chloroplast sequence from FASTQ files

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

fastq assembly

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written 10.0 years ago by Ric

1 answer

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.

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written 10.0 years ago by GenoMax

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