Stampy

Description

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model.

License

See chapter 12 License in the documentation

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 stampy and load default version of stampy as

module avail stampy/ # list available modules
module load stampy   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail stampy

and choose explicit version you want to use.

Documentation

https://www.well.ox.ac.uk/files-library/readme.txt

Homepage

https://www.well.ox.ac.uk/research/research-groups/lunter-group/softwares/stampy