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Old 10-30-2015, 11:01 AM   #1
cmccabe
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Default bbduk and kmer masking

Using bbduk on Illumina PE hg19 fastq files from NextSeq. I have done adapter removal, quality trimming and contamination filtering. Is kmer masking needed or recommended before I align using bbmap? Thank you .
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Old 10-30-2015, 11:09 AM   #2
Brian Bushnell
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Quote:
Originally Posted by cmccabe View Post
Using bbduk on Illumina PE hg19 fastq files from NextSeq. I have done adapter removal, quality trimming and contamination filtering. Is kmer masking needed or recommended before I align using bbmap? Thank you .
Nope! That's just for special use-cases.
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Old 10-30-2015, 11:16 AM   #3
cmccabe
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Thank you .

The bbMap tools are amazingly fast and accurate.
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