RAUR is to re-align the reads that can not be mapped by alignment tools. It takes advantages of the base quality scores (reported by the sequencer) to figure out the longest segment of a read with at most K low quality bases. Combined with an alignment tool (like bwa or bowtie2), RAUR re-align the trimmed reads.
- Windows / Linux
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BMC Bioinformatics. 2015 Mar 18;16 Suppl 5:S8. doi: 10.1186/1471-2105-16-S5-S8. Epub 2015 Mar 18.
Re-alignment of the unmapped reads with base quality score.
Peng X, Wang J, Zhang Z, Xiao Q, Li M, Pan Y.