RapMap
Description
RapMap is a testing ground for ideas in lightweight / quasi / pseudo transcriptome alignment. That means that, at this point, it is somewhat experimental and there are no guarantees on stability / compatibility between commits. 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.
License
GNU GPL 3
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of rapmap and load default version of rapmap as
module avail rapmap/ # list available modules module load rapmap # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail rapmap
and choose explicit version you want to use.
Documentation
https://github.com/COMBINE-lab/RapMap