Looking for easy to use eukaryotic genome annotation pipeline?

Question

[goatsrunfaster]

I am trying to annotate a eukaryotic genome but every pipeline I find seems convoluted and complex. All I really have is a fish assembly in fasta format. I am simply looking for pipeline suggestions, ideally that I can install with conda, that also have an easy to understand tutorial. I usually work with bacterial assemblies which are much easier to deal with...

[lieven.sterck]

that must have been an eye-opener indeed when you come from the bacterial (genome annotation) field :) .

anyway, what pipelines have you come across? and why don't you 'like' them?

part of which these pipelines are convoluted and sometimes complex is because eukaryotic genome annotation is complex! Most of them will unfortunately involve some skills and knowledge.

You might want to get a look here: List of genome annotation tools (>140) , a post from Juke34 ,quite complete list of tools and pipelines.

[Dunois]

Is there an equivalent list for transcriptome annotation tools/pipelines?

[lieven.sterck]

good question, perhaps ask Juke34 ;-)

often people rely on 'bacterial' approaches as transcriptome is (or should be ) all single frame, single "exon" (== resembling prokaryotic )

If I remember correctly , in the original Trapid paper there was a comparison with other tools/pipelines.

[goatsrunfaster]

Using maker seems like the way to go, thanks for the info!

[lieven.sterck]

possibly, though I then wonder which pipelines you came across before, as usually Maker is one of the first to pop up.

Answer 1

[colindaven]

Start with Maker (when using transcripts from RNA-seq for evidence) and also Gmap (map transcripts) using their excellent GFF3 output.

Those both give alternative but pretty good output.