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BMCBI
2011

A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping

10 years 3 months ago
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping
Background: Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. Results: We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. Conclusions: We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan. de/projects/rabema.html. 1 Backgrou...
Manuel Holtgrewe, Anne-Katrin Emde, David Weese, K
Added 24 Aug 2011
Updated 24 Aug 2011
Type Journal
Year 2011
Where BMCBI
Authors Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert
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