Originally posted by GenoMax
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Rather than doing the filtering you should consider normalizing your data. For this BBMap has another program called bbnorm.sh. You can find a guide here.
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Trimming stringency w/ excessive data
I'm in the process of assembling a 500Mb animal genome and have both Illumina and PacBio data to work with using a hybrid assembly approach. Generally when I assemble de novo transcriptomes or genomes, I try to not be too "aggressive" with my quality trimming parameters for raw Illumina reads, running something along the lines of:
Code:bbduk.sh in=file1.fq in2=file2.fq out=trimmed.fq qtrim=rl trimq=10 (plus some adapter trimming parameters)
Code:bbduk.sh in=file1.fq in2=file2.fq out=trimmed.fq qtrim=rl trimq=15
Last edited by adamrork; 12-12-2019, 08:49 PM.
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