title: Updates to the RMAP short-read mapping software.
abstract: CONCLUSIONS
  We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads.
  
  
  BACKGROUND
  The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms.
  
  
  BACKGROUND
  andrewds@usc.edu; mzhang@cshl.edu
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA. andrewds@usc.edu
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Smith
authors.forename: Wen-Yu
authors.initials: WY
authors.lastname: Chung
authors.forename: Emily
authors.initials: E
authors.lastname: Hodges
authors.forename: Jude
authors.initials: J
authors.lastname: Kendall
authors.forename: Greg
authors.initials: G
authors.lastname: Hannon
authors.forename: James
authors.initials: J
authors.lastname: Hicks
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software