Accuracy, speed and error tolerance of short DNA sequence aligners

Ziemann, Mark 2016, Accuracy, speed and error tolerance of short DNA sequence aligners, bioRxiv, doi: 10.1101/053686.

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Title Accuracy, speed and error tolerance of short DNA sequence aligners
Author(s) Ziemann, MarkORCID iD for Ziemann, Mark
Journal name bioRxiv
Total pages 19
Publisher Cold Spring Harbor Laboratory Press
Place of publication Cold Spring Harbor, N.Y,
Publication date 2016-05-16
Keyword(s) high throughput sequencing
short read aligners
DNA alignment
Summary Aligning short DNA sequence reads to the genome is an early step in the processing of many types of genomics data, and impacts on the fidelity of downstream results. In this work, the accuracy, speed and tolerance to errors are evaluated in read of varied length for six commonly used mapping tools; BWA aln, BWA mem, Bowtie2, Soap2, Subread and STAR. The accuracy evaluation using Illumina-like simulated reads showed that accuracy varies by read length, but overall BWA aln was most accurate, followed by BWA mem and Bowtie2. BWA mem was most accurate with Ion Torrent-like read sets. STAR was at least 5 fold faster than Bowtie2 or BWA mem. BWA mem tolerated the highest density of mismatches and indels compared to other mappers. These data provide important accuracy and speed benchmarks for commonly used mapping software.
Language eng
DOI 10.1101/053686
ERA Research output type X Not reportable
Copyright notice ©2016, The Author
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