TransLiG

Description

TransLig is an efficient genome-guided trascriptome assembler for RNA-seq data. It can assemble all transcripts from short paired-end reads using a reference genome and analyze their abundances. The software expects as input alignment file by Tophat2 BAM format, and ouput all assembled candidate transcripts in gtf format.

License

This software is free, open-source software released under the GNU General Public 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 translig and load default version of translig as

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

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

module avail translig

and choose explicit version you want to use.

Assemble [--reads/--kmers] <filename>  [opts]

Documentation

Assemble --help

Homepage

https://sourceforge.net/projects/transcriptomeassembly/files/