Introduction

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.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.jwala@broadinstitue.org ; rameen@broadinstitute.org.

Publications

  1. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.
    Cite this
    Wala J, Beroukhim R, 2017-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Jeremiah Wala
    Developer

    Department of Cancer Biology, Dana-Farber Cancer Institute, United States of America

  2. Rameen Beroukhim
    Investigator

    Department of Cancer Biology, Dana-Farber Cancer Institute, United States of America

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Summary
AccessionBT006714
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRameen Beroukhim