SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.
| Authors | |
| Abstract | We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. AVAILABILITY AND IMPLEMENTATION: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. CONTACT: jwala@broadinstitue.org; rameen@broadinstitute.org. |
| Year of Publication | 2016
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| Journal | Bioinformatics
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| Date Published | 2016 Dec 22
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| ISSN | 1367-4811
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| DOI | 10.1093/bioinformatics/btw741
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| PubMed ID | 28011768
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| Links | |
| Grant list | R01 CA188228 / CA / NCI NIH HHS / United States
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