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==
 
==Required Modules==
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===Serial===
 
===Serial===
 
*{{#var:app}}
 
*{{#var:app}}
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
 +
* 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
 
+
<!--Additional-->
===Note:===
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{{#if: {{#var: exe}}|==Additional Information==
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:{{#var:app}}}}_DIR - installation directory
 
<!--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:
 
  cp $HPC_TGICL_CONF/tgicl.cfg .
 
  cp $HPC_TGICL_CONF/tgicl.cfg .
* To get a full list of tgicl commands:
 
perldoc tgicl
 
 
* Sample run
 
* Sample run
 
  tgicl -F sample.fasta  -q sample.qual -c 4
 
  tgicl -F sample.fasta  -q sample.qual -c 4

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

Required Modules

modules documentation

Serial

  • tgicl

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
tgicl -F sample.fasta  -q sample.qual -c 4