Skip to content

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.

To copy a default tgicl.cfg file to your working directory run:

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 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