ATRAM

Description

atram website  

aTRAM does targeted de novo assembly of loci from paired-end Illumina runs and consists of the following tools:

• format_sra.pl: this script creates an aTRAM database from an Illumina paired-end short-read archive.
• aTRAM.pl: this script runs aTRAM with a target sequence and the formatted short-read archive.

Environment Modules

Run module spider atram to find out what environment modules are available for this application.

System Variables

• HPC_ATRAM_DIR - installation directory

Citation

If you publish research that uses atram you have to cite it as follows:
Allen, JM, DI Huang, QC Cronk, KP Johnson. 2015\. aTRAM automated target restricted assembly method a fast method for assembling loci across divergent taxa from next-generation sequencing data. BMC Bioinformatics 16:98 DOI 10.1186/s12859-015-0515-2