NAME

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

SYNOPSIS

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

DESCRIPTION

       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.

OPTIONS

       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))

AUTHOR

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