Difference between revisions of "Eukulele"
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| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
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# A database<sup>1</sup> to which to align the contigs from the metagenome or metatranscriptome. | # A database<sup>1</sup> to which to align the contigs from the metagenome or metatranscriptome. | ||
| − | <sup>1</sup> | + | <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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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| − | * HPC_{{uc:{{#var:app}}}} | + | * 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: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Usage: $ EUKulele --help | |
| + | |||
| + | Example command: | ||
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| + | $ EUKulele --sample_dir ./metatranscriptomes/ -m mets --database mmetsp --reference_dir ${HPC_EUKULELE_MMETSP_DB} --CPUs ${SLURM_CPUS_PER_TASK} | ||
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{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | + | WRITE_POLICY_INFORMATION_HERE | |
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Latest revision as of 22:12, 8 March 2024
Description
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 database1 to which to align the contigs from the metagenome or metatranscriptome.
1As 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.
Environment Modules
Run module spider eukulele to find out what environment modules are available for this application.
System Variables
- HPC_EUKULELE_DIR - installation directory
- HPC_EUKULELE_BIN - executable directory
- HPC_EUKULELE_EUKPROT_DB - EukProt database directory
- HPC_EUKULELE_EUKZOO_DB - EukZoo database directory
- HPC_EUKULELE_MMETSP_DB - MMETSP database directory
- HPC_EUKULELE_PHYLODB_DB - PhyloDB database directory
Additional Information
Usage: $ EUKulele --help
Example command:
$ EUKulele --sample_dir ./metatranscriptomes/ -m mets --database mmetsp --reference_dir ${HPC_EUKULELE_MMETSP_DB} --CPUs ${SLURM_CPUS_PER_TASK}
Citation
If you publish research that uses eukulele 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