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2.3 years ago
ipb727258 • 0
I have assembled contigs by using valvet and got 335 contigs, then my question is : how can I get scaffold, or how can I get single contig? I tried to mapp this contigs to the reference genome but the problem was that consesus sequence produced contains a lots of unknow bases( indicated by ????????), and it is difficult to know a closer related reference?
How can I submit in Gene bank? can I submit contigs or consesus sequence , I am vey confused so much
plz help me guys
Genome assembly is not that easy, what did you assemble? how was your coverage? what tech? paired or single reads? how depth? I guess you mean Velvet assembler, why velvet?
The scaffolding will depend if you have paired/mate pairs in your libraries, otherwise, you will get just contigs.
If you have a reference genome, use that instead of de novo assembly, search for reference-guided assembly.
Genbank has pages about how to submit data.
Spades assembly with different K mers may reduce the contigs size. Moreover, Ragoo or RagTag may help in scaffolding of the assembled with a suitable reference.