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Genome Annotation on a newly sequenced genome

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?

genome assembly
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updated by colindaven colindaven • written by B- for bioinformatics • B- for bioinformatics

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

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written by Friederike Friederike

2 answers

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

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written by Charles Warden Charles Warden

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.

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written by colindaven colindaven

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