can this tool predict genes for a fungi assembly?

raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

BSD 3-Clause "New" or "Revised" License

48 stars 7 forks source link

can this tool predict genes for a fungi assembly? #14

Closed davidmadariaga closed 6 months ago

davidmadariaga commented 6 months ago

it contains 29 contigs, and the size is of 40 mb approximately. Thanks in advance, and sorry if this is a stupid question and sorry also if this part of your github is not for this kind of questions.

Greetings from Chile!

raw-lab commented 6 months ago

Should be able too. Use the fraggenescan setting with the ko eukaryotes. Should have 1.3 update soon. It will have more databases.

davidmadariaga commented 6 months ago

omg thank you!!!!!!!!!! may the universe bless you

davidmadariaga commented 6 months ago

wait, it will probably predict more genes of the assembly if you add it fungal databases, right?

raw-lab commented 6 months ago

Youre too kind. Give it a go and let us know? We will have a major update soon with more databases.

davidmadariaga commented 6 months ago

ok, i will keep you informed, thanks again!!! :D

raw-lab commented 6 months ago

Very welcome! Let us know how it worked out for you! If you want us to include custom or other databases or tools related to your work - please let us know? Closing for now.

We will let you know when 1.3 is completed.

davidmadariaga commented 4 months ago

Hi! it worked!!!!

raw-lab commented 4 months ago

Did you get 1.3 installed? You send the contigs over correct? Do you still want us to annotate for you?

Also, have you run our tool metaome stats? https://github.com/raw-lab/metaome_stats

It will evaluate your assemblies for you.

Let us know?

We have tested on diatoms, bats, dogs, mouse. Haven't tested on plants. But, should work for fungi. Let us know?

davidmadariaga commented 4 months ago

hi!, yes, i sent the contigs. I used the 1.2 version...the 1.3 includes databases related to fungi? in that case i will update it, but it seems fine for now. I'll have to read the paper in order to better understand the output files haha, but it worked, so i dont think it's necessary that you analyze the assembly, thanks for asking!. I used metaomes, i think it's the default in version 1.2, this is the output, it also seems ok:

davidmadariaga commented 4 months ago

thanks for the feedback, you are so kind!

raw-lab commented 4 months ago

Install MetaCerberus 1.3 version. That is best version. There is a bioconda bug that is taking forever to fix.

davidmadariaga commented 4 months ago

Thanks!