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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Non-fungal genomes? #2

Closed nextgenusfs closed 8 years ago

nextgenusfs commented 8 years ago

There has been some interest (at least 1 person...) that is interested in using funanntoate for non-fungal genome annotation. Anybody else interested? I could probably do something like: arthropods, vertebrate, metazoans, and fungi (essentially the BUSCO clades). This would increase the DB files substantially....

nextgenusfs commented 8 years ago

as of v0.3.0 non-fungal organisms might work. In funannotate predict you can use the --organism other option to disable fungal specific prediction steps. You can also use the --busco_db and --eggnog_db options to specify valid busco and eggnog databases. If the local databases do not exist, funannotate will download and format them for you on the fly.

abpatel2288 commented 8 years ago

I am planning for annotation of cattle genome, will it work this --organism other option ? Do I need to modify any other database.

nextgenusfs commented 8 years ago

Hi @abpatel2288. It potentially should work, although I have not tested it. You will also want to adjust the --busco_db, --busco_seed_species, and --max_intronlen, if you do not have other data, such as RNA-seq/assembled transcriptome. If you have a transcriptome and RNAseq reads, then funannotate will use BRAKER1 to train augustus, however you should still specify the --busco_db metazoa to download the proper database.

See https://github.com/nextgenusfs/funannotate/issues/16 here for a related answer on arthropods.

nextgenusfs commented 8 years ago

support for non-fungal genomes is currently in alpha (i.e. I think it works but have not tested it).