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Updates to the RMAP short-read mapping software.

SUMMARY: 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. AVAILABILITY: The applications described in this note are available for download at and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms. CONTACT:;

Pubmed ID: 19736251


  • Smith AD
  • Chung WY
  • Hodges E
  • Kendall J
  • Hannon G
  • Hicks J
  • Xuan Z
  • Zhang MQ


Bioinformatics (Oxford, England)

Publication Data

November 1, 2009

Associated Grants

  • Agency: NCI NIH HHS, Id: P01 CA013106
  • Agency: NCI NIH HHS, Id: T32 CA00917631
  • Agency: NIEHS NIH HHS, Id: U01 ES017166
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Algorithms
  • Computational Biology
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Software