rapmap - rapid sensitive and accurate DNA read mapping via quasi-mapping

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

rapmap 0.3.0                                     September 2016                                        RAPMAP(1)

       RapMap  is  a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment.
       That means that, at this point, it is somewhat experimental. The develop  branch  will  have  the  latest
       improvements  and  additions, but is not guaranteed to be stable between commits. Breaking changes to the
       master branch will be accompanied by a tag to the version before the breaking change.  Currently,  RapMap
       is  a  stand-alone  quasi-mapper  that  can  be  used  with other tools. It is also being used as part of
       Sailfish and Salmon. Eventually, the hope is to create and stabilize an API so that it can be used  as  a
       library from other tools.

       rapmap - rapid sensitive and accurate DNA read mapping via quasi-mapping

       Rapmap contains 4 subcommands:

              pseudoindex - builds a k-mer-based index (see rapmap_pseudoindex(1))

              pseudomap - map reads using a k-mer-based index (see rapmap_pseudomap(1))

              quasiindex - builds a suffix array-based (SA) index (see rapmap_quasiindex(1))

              quasimap - map reads using the SA-based index (see rapmap_quasimap(1))

rapmap[pseudoindex|pseudomap|quasiindex|quasimap]<options>