rapmap1
Rapid sensitive and accurate dna read mapping via quasi-mapping
Usage
rapmap [{pseudoindex | pseudomap | quasiindex | quasimap}]
<options>
Overview
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:
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pseudoindex - builds a k-mer-based index (see rapmap_pseudoindex(1)) |
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pseudomap - map reads using a k-mer-based index (see rapmap_pseudomap(1)) |
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quasiindex - builds a suffix array-based (SA) index (see rapmap_quasiindex(1)) |
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quasimap - map reads using the SA-based index (see rapmap_quasimap(1)) |
Releases
Unchanged in 5 releases since Debian 9 (Stretch).