Annotation of Complex genomes using NCBI Genome Workbench

Question

[SAsciences]

We have sequenced a eukaryotic genome (~32Mb size) and submitted the assembly sequences (chromosomes) to NCBI. Now while performing annotation of the assembly, first we used MAKER to generate gff3 file of the chromosome. Next, to generate .SQN file (for submitting the annotation to NCBI), we used NCBI Genome Workbench software. The Genome Workbench generates .SQN file, but it does not incorporate the features (i.e., genes, cds, exon etc. from the gff3 file) into the resultant SQN file, resulting in a malformed or annotation-less SQN file.

Can anyone please suggest the possible reason and solution of it.

Thanks

Answer 1

[Lissa Cruz Saavedra]

Hi

Recently, I used https://www.gensas.org/ to make the annotation. It was pretty practical and in my opinion easy. You just need to upload your genome an some evidence from RNAseq or protein. It executes different approaches for structural and functional annotation that you can filter at the end .