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--> | ||
| − | == | + | |
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * 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 | ||
Latest revision as of 20:47, 12 August 2022
Description
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
Environment Modules
Run module spider tgicl to find out what environment modules are available for this application.
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
launch_tgicl tgicl -F sample.fasta -q sample.qual -c 4