SOAPindel: efficient identification of indels from short paired reads.
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ABSTRACT:
SUBMITTER: Li S
PROVIDER: S-EPMC3530679 | biostudies-literature | 2013 Jan
REPOSITORIES: biostudies-literature
Publications
SOAPindel: efficient identification of indels from short paired reads.
Li Shengting S Li Ruiqiang R Li Heng H Lu Jianliang J Li Yingrui Y Bolund Lars L Schierup Mikkel H MH Wang Jun J Wang Jun J
Genome research 20120912 1
We present a new approach to indel calling that explicitly exploits that indel differences between a reference and a sequenced sample make the mapping of reads less efficient. We assign all unmapped reads with a mapped partner to their expected genomic positions and then perform extensive de novo assembly on the regions with many unmapped reads to resolve homozygous, heterozygous, and complex indels by exhaustive traversal of the de Bruijn graph. The method is implemented in the software SOAPind ...[more]
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