A set of tools to take fungal genomes mine them for natural products, compare them using phylogenomics, cores, pangenomes. Fun As in Fungi
Dependencies:
AUGUSTUS (3.4.0) a gene prediction tool. Sources and documentation at https://github.com/Gaius-Augustus/Augustus
Antismash Genome annotation tool specilaized in Natural products https://docs.antismash.secondarymetabolites.org/install/
CORASON The version in this repository https://github.com/pablo-genomes-to-vials-cruz/myCORASON
How to use it:
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Sequence and assamble some genomes or download them. Use a fasta file
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Define a taxonomic affiliation for your genome: E. g. Exophiala, create a gene model for it Division: Ascomycota Class: Chaetothyriomycetes Order: Chaetothyriales Family: Herpotrichiellaceae Genus: Exophiala Train a model for annotation (I have some premade already -see repository- ) detailed instructions are available in the Augustus manual E.g the closest annotated reference genome in the Genbanks is Exophiala dermatitidis
NW_008751646 Exophiala dermatitidis NIH/UT8656 Therefore: export AUGUSTUS_CONFIG_PATH=/home/ynp/Augustus/config perl new_species.pl --species=Exophiala dermatitidis etraining --species=Exophiala_dermatitidis NW_008751646.gbk
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Run Augustus to call the genes: augustus --species=Exophiala_dermatitidis mygenome.fna --gff3=on --stopCodonExcludedFromCDS=off > mygenome.gff
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Run antismash to annotate the genes and find natural products BGCs conda activate antismash (if you use conda to run antismash locally) antismash --taxon fungi --fullhmmer --genefinding-gff3 mygenome.gff mygenome.fna
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Integrate the outputs into CORASON-formatted files (the gbk file is the antismash whole genome file e.g. mysequence.gbk perl GFF_GBK_to_FUNGISON_2.pl mysequence.gff mysequence.gbk
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Use this file to run corason
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Enjoy