EVM super-beginner

[peachan...@gmail.com]

Dear EVM team,

I have some doubts regarding how to use EVM.

From the tutorial I gather that I need to provide the software with the genome in fasta format and the rest of files (alignment evidences) in gff3 format. 

I have started the annotation of a genome with MAKER. I used as input the genome, proteins and ESTs. As outputs I got a .gff file with all annotations and evidence alignments, as well as a protein.fasta and ESTs.fasta files. 

My question is: how can I produce the different (e.g. protein, transcript) evidence files in .gff format?

Thank you so much!

Best,

Linnie 

[Brian Haas]

Hi Linnie,

Maker might have EVM integration.  I'd suggest checking with the Maker developers.  If you need certain format converters, there's some in the evm utils directory.   There's no fully supported workflow, though... it's up to the user to match the formatting requirements.   I continue to maintain the code, but I'm not actively developing it anymore.

best,

~brian

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[peachan...@gmail.com]

Hi Brian,

Thanks a lot for your answer! I will make sure to contact the maker developers. 

Best,

Linnie

On Thursday, 11 October 2018 17:50:10 UTC+2, Brian Haas wrote:

Hi Linnie,

Maker might have EVM integration.  I'd suggest checking with the Maker developers.  If you need certain format converters, there's some in the evm utils directory.   There's no fully supported workflow, though... it's up to the user to match the formatting requirements.   I continue to maintain the code, but I'm not actively developing it anymore.

best,

~brian

On Thu, Oct 11, 2018 at 10:19 AM <peachan...@gmail.com> wrote:

Dear EVM team,

I have some doubts regarding how to use EVM.

From the tutorial I gather that I need to provide the software with the genome in fasta format and the rest of files (alignment evidences) in gff3 format. 

I have started the annotation of a genome with MAKER. I used as input the genome, proteins and ESTs. As outputs I got a .gff file with all annotations and evidence alignments, as well as a protein.fasta and ESTs.fasta files. 

My question is: how can I produce the different (e.g. protein, transcript) evidence files in .gff format?

Thank you so much!

Best,

Linnie 

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[Craig Jackson]

Hi Linnie,

You may want to check out the funannotate pipeline, which is a complete genome annotation pipeline (gene prediction and funcational annotation) that uses EVM, (and trinity, PASA, augustus, genemark, etc). 

It produces transcript, protein evidence, etc .gff and .fa like you wanted to produce, from the EVM output and other software.

It also produces NCBI submission ready output as well, which is useful if you plan on submitting genome to NCBI database.

https://github.com/nextgenusfs/funannotate

https://funannotate.readthedocs.io/en/latest/

It can be a bit daunting to install, but I managed with anaconda/bioconda combined with some modules already installed on my cluster and a few manual dependency installations.

Cheers,

Craig

[Brian Haas]

Sounds neat!  Uses much of my tool stack.  🤗

-Brian

(by iPhone)

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