Scaffolding Without Paired Read Information

Question

[lelle]

Here is waht I want to do:

I have an assembly (N50: 5774) from 454 data of a cyano bacteria genome of approximately 7Mb. As all my reads are sinlge end, I can not use mate pair information for scaffolding. However I have three genomes from related (same genus) sepcies. So I would like to use this information for scaffolding. My expirence with genome assemblies is very limited so I am not sure if this is even possible.

So my question is: Does it make sense to use genomes from realted (same genus) species to do scaffolding for a bacterial genome and if so, which tools could I use for that?

[sentausa]

Why do you want to do scaffolding? Are your contigs not enough? I agree with SES that you can try to fill gaps between contigs by mapping your reads to the corresponding region in the related genome.

You might want to see this thread too: How can i do scaffolding with the single end data ?

[lelle]

Its just a case of: "Here are reads. Please assemble the genome." My "clients" will just not be happy if I tell them: "Sorry, you should have done a paired end library, if you want anything near to a complete genome."

[sentausa]

Well, so you can try filling the gaps based on the related genomes as suggested. But don't expect too much if it turns out that the reads can't be mapped to the related genome segment since the genomes have evolved quite differently. At least, you might have your contigs "extended".

Answer 1

[SES]

You can order your contigs relative to a reference with ABACUS, and then try to fill gaps. However, you cannot do scaffolding with single-end reads.