SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly | Zendy

Jeremiah A. Wala | Zendy; Rameen Beroukhim | Zendy

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SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

Author(s) -

Jeremiah A. Wala,

Rameen Beroukhim

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw741

Subject(s) - computer science , sequence (biology) , mit license , file format , interface (matter) , sequence alignment , benchmarking , line (geometry) , license , operating system , biochemistry , chemistry , genetics , business , geometry , mathematics , bubble , marketing , maximum bubble pressure method , gene , peptide sequence , biology

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.

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