Question: Looking for easy to use eukaryotic genome annotation pipeline?
0
gravatar for goatsrunfaster
8 weeks ago by
goatsrunfaster20 wrote:

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...

assembly • 138 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by goatsrunfaster20

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by lieven.sterck8.9k

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

ADD REPLYlink written 8 weeks ago by Dunois160
1

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by lieven.sterck8.9k

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

ADD REPLYlink written 8 weeks ago by goatsrunfaster20

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

ADD REPLYlink written 8 weeks ago by lieven.sterck8.9k
1
gravatar for colindaven
8 weeks ago by
colindaven2.5k
Hannover Medical School
colindaven2.5k wrote:

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.

ADD COMMENTlink written 8 weeks ago by colindaven2.5k
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