scaffolding denovo contigs to genome

Question

[iraun]

Hi there,

I've build some contigs from using unmapped reads. Now, what I want to do is to see if any of those contigs can be included in the reference chromosomes. I've paired end reads and I was thinking about mapping and doing scaffolding with those reads than one end maps to a denovo contig and the other to reference chromosome... But I'm not sure about if this is a correct way to do it and also what software could I use for this...something like SGA?

I hope it is somehow clear!

Thanks in advance

Answer 1

[SES]

Just to add to Istvan's answer, if you want to also compare your contigs to a reference (in addition to scaffolding) you can use mummer or bwa-mem. If you are trying to achive some kind of gap-filling using a reference, take a look at the PAGIT pipeline. Within the PAGIT pipeline there is a program called ABACUS that will orient your contigs relative to the reference, and IMAGE (also part of PAGIT) can be used to fill the gaps.

[iraun]

Thanks SES, I think that ABySS is an assembler.. only to create contigs, not scaffolds.. but I'll take a look to PAGIT pipeline to get some ideas...thanks!

[SES]

You are correct about ABYSS, I was thinking of ABACAS and I updated my answer to clarify.

Answer 2

[Istvan Albert]

You can try tools like SSPACE that was designed to help scaffold contigs with paired end reads

[iraun]

This tool is nice, but I think that you have to pay to get the last version...so... :S