TGICL
Description
TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets.
This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3. Both clustering and assembly phases can be parallelized by distributing the searches and the assembly jobs across multiple CPUs, as TGICL can take advantage of either SMP machines or PVM (Parallel Virtual Machine) clusters. The two full precompiled packages below were built on Linux and SunOS, respectively. They include CAP3, mgblast and all the other binaries for this platform (of course, except the base Unix utilities like 'sed', 'sort' etc.).
License
The Artistic licence
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 TGICL and load default version of TGICL as
module avail TGICL/ # list available modules module load TGICL # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail TGICL
and choose explicit version you want to use.
Adding of module will copy configuration file /software/TGICL-2.1/build/etc/tgicl.cfg to the actual directory. This cfg file must be edited.
Documentation
https://sourceforge.net/projects/tgicl/