Difference between revisions of "ATRAM"

From UFRC
Jump to navigation Jump to search
Line 63: Line 63:
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} 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
+
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  
 
|}}
 
|}}
 
<!--Installation-->
 
<!--Installation-->

Revision as of 16:01, 27 May 2022

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.

Required Modules

Serial

  • atram

System Variables

  • HPC_ATRAM_DIR




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


Validation

  • Validated 4/5/2018