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

    loading  Checking for direct PDF access through Ovid


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 SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license.


Related Topics

    loading  Loading Related Articles