BIMA V3: An aligner customized for mate pair library sequencing

Travis M. Drucker, Sarah H. Johnson, Stephen J. Murphy, Kendall W. Cradic, Terry M. Therneau, George Vasmatzis

Research output: Contribution to journalArticle

50 Scopus citations

Abstract

Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate-pair read pairs to a reference genome is a challenging and time-consuming process for most next-generation sequencing alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and presence of structural variant breakpoints within reads increase mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular next-generation sequencing alignment programs when processing mate pair sequencing.

Original languageEnglish (US)
Pages (from-to)1627-1629
Number of pages3
JournalBioinformatics
Volume30
Issue number11
DOIs
StatePublished - Jun 1 2014

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'BIMA V3: An aligner customized for mate pair library sequencing'. Together they form a unique fingerprint.

  • Cite this