Difference between revisions of "ATRAM"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Math]] |
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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. | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==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