View source for Finder

[[Category:Software]]
[[Category:Biology]]
[[Category:Bioinformatics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|finder}}
|{{#vardefine:url|https://github.com/sagnikbanerjee15/Finder}}
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|{{#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-->
|}
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

finder is a gene annotator pipeline which automates the process of
downloading short reads, aligning them and using the assembled transcripts
to generate gene annotations. Additionally it uses protein sequences and
reports gene predictions by BRAKER2. It is a fast, scalable, platform
independent software that generatess gene annotations in GTF format. finder
accepts inputs through command line interface. It finds several novel
genes/transcripts and also reports the tissue/conditions they were found
to be in.

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==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
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==

WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY

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<!--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

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<!--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:

Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z Sen,Roger P Wise, and Carson M Andorf. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.bioRxiv, page 2021.02.04.429837, 2 2021.

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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