Difference between revisions of "Tgicl"

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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
+
  tgicl -F sample.fasta  -q sample.qual -c 4
 
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Revision as of 18:34, 20 March 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_{{#uppercase: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