I would like to remove mitochondrial, chloroplast and rDNA contaminants from read data using BBTools - I was wondering if anyone has used BBTools to do this and can share the generic pipeline.
Thanks in advance.
Thanks in advance.
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bbmap.sh in=read_1.fq.gz ref=rRNA_Chlor_Mito.fa maxindel=1 minid=0.95 outu=clean_read_1.fq.gz nodisk
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