NAME

rapmap_quasimap - rapmap module to map reads using the SA-based index

SYNOPSIS

rapmap quasimap [-c] [-f] [-s] [-m <positive integer>] [-t <positive integer>] [-o <path>] [-r <path>] [-2 <path>] [-1 <path>] [-n] -i <path> [--] [--version] [-h]

DESCRIPTION

RapMap Mapper (SA-based)

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

-c, --consistentHits

Ensure that the hits collected are consistent (co-linear)

-f, --fuzzyIntersection

Find paired-end mapping locations using fuzzy intersection

-s, --strictCheck

Perform extra checks to try and assure that only equally "best" mappings for a read are reported

-m, --maxNumHits <positive integer>

Reads mapping to more than this many loci are discarded

-t, --numThreads <positive integer>

Number of threads to use

-o, --output <path>

The output file (default: stdout)

-r, --unmatedReads <path>

The location of single-end reads

-2, --rightMates <path>

The location of the right paired-end reads

-1, --leftMates <path>

The location of the left paired-end reads

-n, --noOutput

Don't write out any alignments (for speed testing purposes)

-i, --index <path>

(required) The location of the quasiindex

--, --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.