RMAP is aimed to map accurately reads from the next-generation sequencing technology. RMAP can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.
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Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and Zhang MQ (2009)
Updates to the RMAP short-read mapping software.