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Partek Flow software wraps Cutadapt [21], a widely used tool for adapter trimming. It can be used to trim adapter sequences in nucleotide-space data as well as color-space data.
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The third section of advanced options is the Additional modification to reads. The quality cutoff is used to trim bad quality bases from the reads before trimming adapter. Quality encoding tells the quality score encoding for the raw data. The Reads names prefix and suffix is used to add prefix and suffix to the read ID. Lastly, the Negative quality zero if checked will convert all negative quality score base to zero.
References
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011; 17: 10-12.
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