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reformat.sh in=reads.fq out=highQuality.fq maq=16 (that will throw away all reads with average quality below 16) #Filter #BBMap #Quality

Convert interleaved to separate files with BBmap. $ reformat.sh in=reads.fq out1=reads_r1.fq out2=reads_r2.fq #interleave #fastq #seperate #reformat #bbmap