How Can I Obtain Genome Scaffolds Using Paired End 454 Reads And An Hybrid Assembly As Input?

Question

[Luke]

Hi.

I have an hybrid assembly (454 + Illumina) of 268 contigs (genome of about 7Mb).

Now I want to create scaffolds using 3k 454 paired end reads.

Which tool can I use? Newbler? (I would not use MIRA). With Which options?

Any suggestions?

Thanks in advance ;)

Luke

[Gaffa]

Just curious - why not MIRA?

Answer 1

[Richard Smith-Unna]

I would try using SSPACE and GapFiller in that order.

An alternative is to use SGA - see the wiki for instructions.