Difference between revisions of "Eukulele"

Revision as of 17:12, 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/. See usage 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

Specify pre-installed database: e.g.,

$ EUKulele [subroutine] --reference_dir ${HPC_EUKULELE_PHYLODB_DB}

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

@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 32: / Line 32: @@
 # A database<sup>1</sup> to which to align the contigs from the metagenome or metatranscriptome.
-<sup>1</sup>Version-specific preformatted PhyloDB, EukProt, and MMETSP databases are available at the following path: /data/reference/eukulele/
+<sup>1</sup>As a courtesy, HiPerGator hosts version-specific preformatted EukProt, EUKZOO, MMETSP, and PhyloDB databases at the following path: /data/reference/eukulele/. See usage below.
 <!--Modules-->
@@ Line 40: / Line 40: @@
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_{{uc:{{#var:app}}}}_BIN - executable directory
-* HPC_{{uc:{{#var:app}}}}_DB - database 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
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 48: / Line 53: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+Usage: $ EUKulele --help
+Specify pre-installed database: e.g.,
+$ EUKulele [subroutine] --reference_dir ${HPC_EUKULELE_PHYLODB_DB}
 |}}
@@ Line 58: / Line 67: @@
 {{#if: {{#var: policy}}|==Usage Policy==
-WRITE USAGE POLICY HERE (Licensing, usage, access).
+WRITE_POLICY_INFORMATION_HERE
 |}}