SOAPdenovo-trans

Description

SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.

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 osoapdenovo-trans and load default version of osoapdenovo-trans as

module avail osoapdenovo-trans/ # list available modules
module load osoapdenovo-trans   # load (default) module

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

module avail osoapdenovo-trans

and choose explicit version you want to use. Load the module (module add soapdenovo-trans-1.04) and use the available tools (SOAPdenovo-127mer, SOAPdenovo-63mer, SOAPdenovo-31mer) in accordance with the program documentation.

Documentation

Documentation is available on official website. Help and instruction manual is also a part of the package. https://github.com/aquaskyline/SOAPdenovo-Trans

Homepage

URL: http://soap.genomics.org.cn/SOAPdenovo-Trans.html http://soap.genomics.org.cn/