Genome Annotation on a newly sequenced genome

Question

[B- for bioinformatics]

I have to annotate a newly sequenced eukaryotic organism genome. There are different steps involved in it, what would be those steps? What kind of dataset I would need to do a good job?

[Friederike]

You provide fairly little information in your question. You may want to add the type of data you're looking at, the size of the organism's genome (yeast ballpark or platypus?), what type of annotation you would like to generate and so on.

Pubmed is usually a good start to look for reviews about your subject of interest, e.g. Ekblom 2014

Answer 1

[Charles Warden]

You need to take a considerable amount of time to critically assess the results. So, you definitely shouldn't use one annotation result and directly go to publication.

However, one possible option (with multiple parameter settings to test) is MAKER

Answer 2

[colindaven]

Another very helpful alternative to MAKER is Gmap for mapping transcript assemblies (think Cufflinks (old), Trinity, Stringtie etc results) to the genome.

Use the excellent GFF3 output and compare and contrast with MAKER results.