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TGICL

Description

tgicl website

TGICL Software 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.

Environment Variables

  • HPC_TGICL_DIR - installation directory
  • HPC_TGICL_BIN - executable directory
  • HPC_TGICL_CONF - conf directory To copy a default tgicl.cfg file to your working directory run: cp $HPC_TGICL_CONF/tgicl.cfg .

Additional Usage Information

To copy the default skeleton configuration file to the working directory, run the following command: 

cp $HPC_TGICL_CONF/tgicl.cfg .

Here is a sample run command: 

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

Categories

biology, ngs, sequencing