Question: How to annotate eukaryotic genome
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gravatar for goatsrunfaster
7 months ago by
goatsrunfaster20 wrote:

I have a fragmented eukaryotic genome (contigs in fasta format) I would like to annotate (and create a genbank file for if possible). I found The NCBI Eukaryotic Genome Annotation Pipeline page on NCBI, but incredibly I see no information on how to actually run something through that pipeline (I assume I would need to submit the assembly to the database), and it seems like my genome may be too fragmented given their criteria for annotation anyway.

That being said, Are there any command-line tools that will do this for me or another pipeline I might use for this purpose?

assembly genome • 220 views
ADD COMMENTlink written 7 months ago by goatsrunfaster20

You need to contact NCBI by using Request Annotation button/option at top of the page. It is kind of obscure. Once you put a ticket in (the link redirects you to create a ticket) someone from NCBI will get in touch with you to see what your options are.

Here are some of your other options: Annotation pipelines in 2018

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax91k

great thanks, helpful information!

ADD REPLYlink written 7 months ago by goatsrunfaster20

You can find a comprehensive list of annotation tools here https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools.md

ADD REPLYlink modified 7 months ago • written 7 months ago by Juke344.8k
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