funannotate 1.8.1-foss-2019b-Python-3.7.4

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 1.8.1-foss-2019b-Python-3.7.4

To load the module for funannotate 1.8.1-foss-2019b-Python-3.7.4 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load funannotate/1.8.1-foss-2019b-Python-3.7.4

BEAR Apps Version

2020b

Extensions

  • coverage 5.3
  • distro 1.5.0
  • funannotate 1.8.1
  • goatools 1.0.6
  • natsort 7.0.1
  • pydot 1.4.1
  • pytest-cov-2.10.1
  • wget 3.2
  • XlsxWriter 1.3.6

More Information

For more information visit the funannotate website.

Dependencies

This version of funannotate has a direct dependency on: AUGUSTUS/3.3.3-foss-2019b BamTools/2.5.1-GCC-8.3.0 BEDTools/2.29.2-GCC-8.3.0 BioPerl/1.7.2-GCCcore-8.3.0 Biopython/1.75-foss-2019b-Python-3.7.4 BLAT/3.5-GCCcore-8.3.0 CodingQuarry/2.0-GCC-8.3.0 DBD-mysql/4.050-foss-2019b-Perl-5.30.0 DIAMOND/0.9.30-GCC-8.3.0 ETE/3.1.2-foss-2019b-Python-3.7.4 EVidenceModeler/1.1.1-GCCcore-8.3.0 Exonerate/2.4.0-GCC-8.3.0 FASTA/36.3.8h_04-May-2020-foss-2019b foss/2019b GeneMark-ET/4.61-GCCcore-8.3.0 GlimmerHMM/3.0.4c-GCC-8.3.0 GMAP-GSNAP/2020-09-12-foss-2019b HISAT2/2.2.1-foss-2019b kallisto/0.46.1-foss-2019b Kent_tools/401-foss-2019b MAFFT/7.453-GCC-8.3.0-with-extensions matplotlib/3.1.1-foss-2019b-Python-3.7.4 minimap2/2.17-GCC-8.3.0 PASApipeline/2.4.1-foss-2019b Perl/5.30.0-GCCcore-8.3.0 Proteinortho/6.0.23-foss-2019b-Python-3.7.4-Perl-5.30.0 Python/3.7.4-GCCcore-8.3.0 RepeatMasker/4.0.9-p2-gompi-2019b-HMMER RMBlast/2.9.0-gompi-2019b Salmon/1.1.0-gompi-2019b SAMtools/1.10-GCC-8.3.0 scikit-learn/0.21.3-foss-2019b-Python-3.7.4 SciPy-bundle/2019.10-foss-2019b-Python-3.7.4 Seaborn/0.10.0-foss-2019b-Python-3.7.4 SignalP/5.0b SNAP/2013-11-29-GCC-8.3.0 statsmodels/0.11.0-foss-2019b-Python-3.7.4 StringTie/2.1.3-GCC-8.3.0 tantan/23-GCCcore-8.3.0 trimAl/1.4.1-GCC-8.3.0 Trimmomatic/0.39-Java-11 Trinity/2.9.1-foss-2019b-Python-3.7.4 tRNAscan-SE/2.0.6-GCCcore-8.3.0

Other Versions

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

Version BEAR Apps Version
1.8.1-foss-2019b-Python-2.7.16 2019b

Last modified on 12th October 2020