Difference between revisions of "ATRAM"

From UFRC
Jump to navigation Jump to search
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Math]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|atram}}
 
|{{#vardefine:app|atram}}
Line 23: Line 23:
 
* aTRAM.pl: this script runs aTRAM with a target sequence and the formatted short-read archive.
 
* aTRAM.pl: this script runs aTRAM with a target sequence and the formatted short-read archive.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 63: Line 53:
 
{{#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:
 +
<br>
 
[https://bmcbioinformatics.biomedcentral.com/articles/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]
 
[https://bmcbioinformatics.biomedcentral.com/articles/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]
 
|}}
 
|}}
Line 70: Line 61:
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 15:23, 12 August 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.

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