[maker-devel] MAKER annotation submission (EMBLmyGFF3)

[Jacques Dainat]

Hi MAKER users,

I take advantage to this mailing list to share a tool that I hope will be useful for MAKER's users. One of the steps once we are happy of our wonderful annotation is to submit it to the public archives through one of the three INSDC databases (EMBL-EBI / NCBI / DDBJ).
We developed EMBLmyGFF3, allowing to easily convert any kind of GFF3 annotation to the EMBL flat file format in order to submit to the European Nucleotide Archive (ENA) Database that is part of EMBL-EBI.
It works well, amongst others, with the MAKER annotation output. We hope the tool will ease the submission process of your annotations.

You will find it here:
https://github.com/NBISweden/EMBLmyGFF3

A typical usage case will look like that (where ERSXXXXXX and PRJXXXXXX are the accession number and the project ID provided by EMBL-EBI prior to any submission):
./EMBLmyGFF3.py maker.gff3 maker.fa --data_class STD --topology linear --molecule_type 'genomic DNA' --table 1 --species 'Drosophila melanogaster (fly)' --taxonomy INV --accession ERSXXXXXXX --project_id PRJXXXXXXX --rg MYGROUP -o result.embl

Best regards,

Jacques Dainat, PhD
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NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
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Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics


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