Difference between revisions of "TGICL"

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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
 
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
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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[[Modules|modules documentation]]
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
*{{#var:app}}
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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_TGICL_BIN - executable directory
 
* HPC_TGICL_BIN - executable directory
 
* HPC_TGICL_CONF - conf directory
 
* HPC_TGICL_CONF - conf directory

Latest revision as of 21:29, 6 December 2019

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

Environment Modules

Run module spider tgicl to find out what environment modules are available for this application.

System Variables

  • HPC_TGICL_DIR - installation directory
  • HPC_TGICL_BIN - executable directory
  • HPC_TGICL_CONF - conf directory

Additional Information

  • To copy the default skeleton configuration file to the working directory:
cp $HPC_TGICL_CONF/tgicl.cfg .
  • Sample run
launch_tgicl tgicl -F sample.fasta  -q sample.qual -c 4