HAPCUT2
Description
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others
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 hapcut2 and load default version of hapcut2 as
module avail hapcut2/ # list available modules module load hapcut2 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail hapcut2
and choose explicit version you want to use.
Documentation
https://github.com/vibansal/hapcut2