Difference between revisions of "Tgicl"

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*{{#var:app}}
 
*{{#var:app}}
 
==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
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  cp $HPC_TGICL_CONF/tgicl.cfg .
 
  cp $HPC_TGICL_CONF/tgicl.cfg .
 
* Sample run
 
* Sample run
  launch_tgicl tgicl -F sample.fasta  -q sample.qual -c 4
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  tgicl -F sample.fasta  -q sample.qual -c 4
 
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<!--Configuration-->
 
<!--Configuration-->

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