Mitobim

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Description

Mitobim is an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim).

License

The MIT License

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 mitobim and load default version of mitobim as

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


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

module avail mitobim

and choose explicit version you want to use. Then run as

MITObim.pl

Documentation

https://github.com/chrishah/MITObim

Homepage

https://github.com/chrishah/MITObim