View source for YASRA

[[Category:Software]] [[Category:biology]][[Category:NGS]][[Category:sequencing]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|yasra}}
|{{#vardefine:url|http://www.bx.psu.edu/miller_lab/}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ. Special scoring sets were derived to improve the performance, both in runtime and quality for 454 and Illumina sequence reads. 
<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory

<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
|}}
<!--PBS scripts-->
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE_CITATION_HERE
|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
__NOTOC____NOEDITSECTION__