funannotate 1.8.17-foss-2022a

Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process. Funannotate is also a lightweight comparative genomics platform. Genomes that have had functional annotation added via the funannotate annotate command can be run through the funannotate compare script that outputs html based whole genome comparisons. The software can run orthologous clustering, construct whole-genome phylogenies, run Gene Ontology enrichment analysis, as well as calculate dN/dS ratios for orthologous clusters under positive selection.

Accessing funannotate 1.8.17-foss-2022a

To load the module for funannotate 1.8.17-foss-2022a please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2022a
module load funannotate/1.8.17-foss-2022a

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Extensions

  • distro 1.9.0
  • funannotate 1.8.17
  • natsort 8.4.0

More Information

For more information visit the funannotate website.

Dependencies

This version of funannotate has a direct dependency on: AUGUSTUS/3.5.0-foss-2022a BamTools/2.5.2-GCC-11.3.0 BEDTools/2.30.0-GCC-11.3.0 BioPerl/1.7.8-GCCcore-11.3.0 Biopython/1.79-foss-2022a BLAT/3.7-GCC-11.3.0 CodingQuarry/2.0-foss-2022a DBD-mysql/4.050-GCC-11.3.0 DIAMOND/2.1.0-GCC-11.3.0 eggnog-mapper/2.1.9-foss-2022a ETE/3.1.3-foss-2022a EVidenceModeler/2.1.0-GCCcore-11.3.0 Exonerate/2.4.0-GCC-11.3.0 FASTA/36.3.8i-GCC-11.3.0 foss/2022a GeneMark-ET/4.72-GCCcore-11.3.0 GlimmerHMM/3.0.4c-GCC-11.3.0 GMAP-GSNAP/2023-02-17-GCC-11.3.0 GOATOOLS/1.3.1-foss-2022a HISAT2/2.2.1-gompi-2022a kallisto/0.48.0-gompi-2022a Kent_tools/442-GCC-11.3.0 MAFFT/7.505-GCC-11.3.0-with-extensions matplotlib/3.5.2-foss-2022a minimap2/2.24-GCCcore-11.3.0 PASA/2.5.2-foss-2022a Perl/5.34.1-GCCcore-11.3.0 Proteinortho/6.2.3-gompi-2022a Python/3.10.4-GCCcore-11.3.0 RepeatMasker/4.1.5-foss-2022a RMBlast/2.13.0-gompi-2022a Salmon/1.9.0-GCC-11.3.0 SAMtools/1.16.1-GCC-11.3.0 scikit-learn/1.1.2-foss-2022a SciPy-bundle/2022.05-foss-2022a Seaborn/0.12.1-foss-2022a SignalP/6.0h-foss-2022a-fast SNAP/2.0.1-GCC-11.3.0 statsmodels/0.13.1-foss-2022a StringTie/2.2.1-GCC-11.3.0 tantan/49-GCC-11.3.0 trimAl/1.4.1-GCCcore-11.3.0 Trimmomatic/0.39-Java-11 Trinity/2.15.1-foss-2022a tRNAscan-SE/2.0.11-foss-2022a

Other Versions

These versions of funannotate are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 31st May 2024