Question: scaffolding denovo contigs to genome
1
gravatar for iraun
4.7 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

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
 

denovo scaffolding • 3.6k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 4.7 years ago by iraun3.5k
2
gravatar for SES
4.6 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

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.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by SES8.1k
1

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!

ADD REPLYlink written 4.6 years ago by iraun3.5k

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

ADD REPLYlink written 4.6 years ago by SES8.1k
1
gravatar for Istvan Albert
4.6 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

http://www.baseclear.com/lab-products/bioinformatics-tools/sspace-standard/

ADD COMMENTlink written 4.6 years ago by Istvan Albert ♦♦ 80k
1

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

ADD REPLYlink written 4.6 years ago by iraun3.5k
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