My objective is to construct single sequence genome assembly.
But I have short reads only without long reads. I got multiple contigs out of assembly.
My question is that can I use these contigs along short reads to fill the gap and construct single sequence?
Thankyou!
It's very unlikely. The assembler did the best it could with the short data you have; any gaps that remain cannot be filled using short reads alone. Some options to create a 'single sequence' from your data:
But yeah, short reads alone will never go past the draft assembly stage.
Right Phillip. In reference to option 4, scaffolding will fill the gaps with Ns not bases is it okay? Don't we need to add bases instead ?
Yes Ns are very common in draft genome assemblies.
You'll get them with matepaired reads too: with matepaired data you have 1000 to 5000 bp between R1 and R2, that's enough to scaffold contigs, but the scaffolder will fill the rest with Ns.
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If it's a bacterial genome then most likely contigs will end on rRNA sequences since there are several almost identical copies, it might not be a problem depending on your goals.
So why not do a reference-guided assembly?
Which tool or approach should I use to perform reference guided assembly?