NAME

       rapmap_quasiindex - rapmap module to build a suffix array-based (SA) index

SYNOPSIS

       rapmap  quasiindex  [-x  <positive integer <= # cores>] [-p] [-n] [-k <positive integer less than 32>] -i
       <path> -t <path> [--] [--version] [-h]

DESCRIPTION

       RapMap Indexer

       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

       -x, --numThreads <positive integer <= #cores>
              Use this many threads to build the perfect hash function

       -p, --perfectHash
              Use a perfect hash instead of dense hash --- somewhat slows construction, but uses less memory

       -n, --noClip
              Don't clip poly-A tails from the ends of target sequences

       -k, --klen <positive integer less than 32>
              The length of k-mer to index

       -i, --index <path>
              (required) The location where the index should be written

       -t, --transcripts <path>
              (required) The transcript file to be indexed

       --, --ignore_rest
              Ignores the rest of the labeled arguments following this flag.

       --version
              Displays version information and exits.

       -h,  --help
              Displays usage information and exits.

AUTHOR

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

rapmap_quasiindex 0.3.0                          September 2016                             RAPMAP_QUASIINDEX(1)