SOAPdenovo
Description
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
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 SOAPdenovo2 and load default version of SOAPdenovo2 as
module avail SOAPdenovo2/ # list available modules module load SOAPdenovo2 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail SOAPdenovo2
and choose explicit version you want to use.
Load the module (module add SOAPdenovo2) and use the available tools (Corrector_AR, Corrector_HA, ErrorCorrection, finalFusion, GapCloser, KmerFreq_AR, KmerFreq_HA, SOAPdenovo-127mer, SOAPdenovo-63mer) in accordance with the program documentation.
- version 2.0 r240 (module
SOAPdenovo2) -- SOAPdenovo2 together with other related tools (namely SOAPec, GapCloser, Data prepare and Error Correction modules) - version 1.05 (module
SOAPdenovo) -- SOAPdenovo version 1.05
Documentation
Documentation is available on official website. Help and instruction manual is also a part of the package. https://github.com/aquaskyline/SOAPdenovo2