Updates to the RMAP short-read mapping software.

Abstract:: 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 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. CONTACT: andrewds@usc.edu; mzhang@cshl.edu

Authors:: AD Smith, W-Y Chung, E Hodges, J Kendall, G Hannon, J Hicks, Z Xuan, MQ Zhang

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