title: SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.
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.
  
  
  
  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.
authors.affiliation: The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.|Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA.|Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors.forename: Jeremiah
authors.initials: J
authors.lastname: Wala
authors.affiliation: The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.|Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA.|Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors.forename: Rameen
authors.initials: R
authors.lastname: Beroukhim
mesh_terms: D002875:Chromosomes; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software