Updates to the RMAP short-read mapping software.
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
Smith
Andrew D
AD
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA. andrewds@usc.edu
Chung
Wen-Yu
WY
Hodges
Emily
E
Kendall
Jude
J
Hannon
Greg
G
Hicks
James
J
Xuan
Zhenyu
Z
Zhang
Michael Q
MQ
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software