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.