View source for NtEdit

[[Category:Software]][[Category:Phylogenetics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|ntedit}}
|{{#vardefine:url|https://github.com/bcgsc/ntEdit}}
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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|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

ntEdit is a scalable genomics application for polishing genome assembly drafts. ntEdit simplifies polishing and "haploidization" of gene and genome sequences with its re-usable Bloom filter design. We expect ntEdit to have additional applications in fast mapping of simple nucleotide variations between any two individuals or species’ genomes.

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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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#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).

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{{#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:

[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz400/5490204 Rene L Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven JM Jones, Jean Bousquet, Joerg Bohlmann, Inanc Birol. 2019. Bioinformatics. doi:10.1093/bioinformatics/btz400]

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