De Novo Assembly from Oligos

Question

[Kenneth]

Hello,

I am trying to assemble a pseudo-chromosome from a few thousand 130bp oligos with 30bp of overlap. I've aligned all of my reads to their reference and I have at least 20X coverage for each oligo. I've tried megahit and spades but I am not quite getting the correct scaffold. Is there an assembler that is more adept at this style of assembly?

If not, is there a tool that can generate consensus reads from NGS data?

Thanks.

[GenoMax]

Perhaps tadpole.sh from BBMap suite may work.

Tadpole guide is available.

[liorglic]

SPAdes should work in this case, so there's either something wrong with your data, or you're using them wrong. Please provide the SPAdes/MEGAHIT commands you ran and explain what you mean exactly by "I am not quite getting the correct scaffold".