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whole genome sequencing data analysis

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

assembly
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written by ipb727258 • ipb727258

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.

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written by JC JC

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.

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written by MSRS MSRS

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