View source for Eukulele

[[Category:Software]][[Category:Alignment]][[Category:Annotation]][[Category:Biology]][[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|eukulele}}
|{{#vardefine:url|https://eukulele.readthedocs.io/}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--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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'''EUKulele''' is a Python program for taxonomic annotation of microbes in metatranscriptomic and metagenomic samples, with special emphasis on eukaryote discovery.

The software includes four major features:

     * Database setup and formatting
     * Database creation, alignment, and taxonomic estimation
     * Assessment of the BUSCO completeness of subsets of contigs at each taxonomic level
     * Assessment of taxonomic classification using only BUSCO-identified core eukaryotic genes

In principle, there are two prerequisites for running the software:

# Metagenomic or metatranscriptomic sample files (unless using the provided sample data)
# A database<sup>1</sup> to which to align the contigs from the metagenome or metatranscriptome.

<sup>1</sup>As a courtesy, HiPerGator hosts version-specific preformatted EukProt, EUKZOO, MMETSP, and PhyloDB databases at the following path: /data/reference/eukulele/. If you do not specify your database path, it will be downloaded unnecessarily to your working directory. Follow usage example below.

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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
* HPC_{{uc:{{#var:app}}}}_EUKPROT_DB - EukProt database directory
* HPC_{{uc:{{#var:app}}}}_EUKZOO_DB - EukZoo database directory
* HPC_{{uc:{{#var:app}}}}_MMETSP_DB - MMETSP database directory
* HPC_{{uc:{{#var:app}}}}_PHYLODB_DB - PhyloDB database 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==

Usage: $ EUKulele --help

Example command: 

$ EUKulele all --m mets --sample_dir ./metatranscriptomes/ --database phylodb --reference_dir ${HPC_EUKULELE_PHYLODB_DB} --CPUs ${SLURM_CPUS_PER_TASK}

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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_POLICY_INFORMATION_HERE

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<!--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:

Krinos AI, Hu SK, Cohen NR, Alexander H. EUKulele: taxonomic annotation of the unsung eukaryotic microbes. J Open Source Softw. 2021;6(57):2817. https://doi.org/10.21105/joss.02817

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