View source for V-pipe

[[Category:Software]]
[[Category:Biology]]
[[Category:Genomics]]
[[Category:Sequencing]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|v-pipe}}
|{{#vardefine:url|https://cbg-ethz.github.io/V-pipe/}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

V-pipe is a workflow designed for analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format.

<!--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

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job 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:

Posada-Céspedes S., Seifert D., Topolsky I., Jablonski K., Metzner K.J., and Beerenwinkel N. 2021. "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data." Bioinformatics, January. doi:10.1093/bioinformatics/btab015.

|}}
<!--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__