RagTag assembly after spades

Question

[anithanagaraj93]

Hello everyone,

I started denovo assembly of yeast (species not known), ran Spades, and got results. But I have doubt in ragtag after Spades, for ragtag need to give contigs/scaffolds as an input? I read about ragtag in Github it showing contings only. Which one to consider?

Thanks and Regards, Anitha

[samuel.a.odonnell]

RagTag, unless recently changed, scaffolds an assembly. Therefore you need to provide it your assembly from Spades, the contigs, alongside a reference... Since your species is unknown this will prove difficult but perhaps you can find the most similar species?