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Accuracy, speed and error tolerance of short DNA sequence aligners

View ORCID ProfileMark Ziemann
doi: https://doi.org/10.1101/053686
Mark Ziemann
Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 16, 2016.
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Accuracy, speed and error tolerance of short DNA sequence aligners
Mark Ziemann
bioRxiv 053686; doi: https://doi.org/10.1101/053686
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Accuracy, speed and error tolerance of short DNA sequence aligners
Mark Ziemann
bioRxiv 053686; doi: https://doi.org/10.1101/053686

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