Difference between revisions of "Tgicl"

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By default loading the module for tgicl also loads the latest Perl and CAP3 modules. The main version of cap3 is used for analyses. If you wish to use the cap3 version distributed with tgicl, it is located at $HPC_TGICL_BIN/cap3.tgicl
 
By default loading the module for tgicl also loads the latest Perl and CAP3 modules. The main version of cap3 is used for analyses. If you wish to use the cap3 version distributed with tgicl, it is located at $HPC_TGICL_BIN/cap3.tgicl
  
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==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 
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{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
* To copy the default skeleton configuration file to the working directory:
 
* To copy the default skeleton configuration file to the working directory:

Revision as of 17:22, 10 August 2012

Description

tgicl website  

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


Required Modules

modules documentation

Serial

  • tgicl
  • HPC_TGICL_BIN - executable directory
  • HPC_TGICL_CONF - conf directory

Note:

By default loading the module for tgicl also loads the latest Perl and CAP3 modules. The main version of cap3 is used for analyses. If you wish to use the cap3 version distributed with tgicl, it is located at $HPC_TGICL_BIN/cap3.tgicl

System Variables

  • HPC_{{#uppercase:tgicl}}_DIR - installation directory

How To Run

  • To copy the default skeleton configuration file to the working directory:
cp $HPC_TGICL_CONF/tgicl.cfg .
  • To get a full list of tgicl commands:
perldoc tgicl
  • Sample run
tgicl -F sample.fasta  -q sample.qual -c 4