TGICL

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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.).

Availability

Version 2.1

Use

module add TGICL-2.1
tgicl

see Documentation.

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/

Licence

The Artistic licence

Program manager

meta@cesnet.cz

Homepage

https://sourceforge.net/projects/tgicl/