ATRAM: Difference between revisions
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[[Category:Software]][[Category: | [[Category:Software]][[Category:Math]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|atram}} | |{{#vardefine:app|atram}} | ||
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* 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--> | ||
== | ==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_{{uc:{{#var:app}}}}_DIR | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#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 | <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] | |||
|}} | |}} | ||
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Latest revision as of 15:23, 12 August 2022
Description
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