Revision as of 11:06, 24 April 2017

Application Details

• Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.
• Version: 2.5.0
• Module: cegma/2.5.0
• Licence: Open source, free to academic research

Usage Examples

CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. We use the KOGs database to build a set of these highly conserved ubiquitous proteins. We define a set of 458 core proteins, and the protocol, CEGMA, to find orthologs of the core proteins in new genomes and to determine their exon-intron structures.

It has the following commands:

• cegma
• completeness
• geneid-train
• genome_map
• hmm_select
• local_map
• make_paramfile parsewise

and is invoke by loading the cegma module within Viper.

Module

[username@login01 ~]$ module add cegma/2.5.0
[username@login01 ~]$ cegma --genome sample.dna --protein sample.prot -o sample

Further Information

• https://support.hdfgroup.org/HDF5/

Home Application support General Training Programming support