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

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

assembly illumina scaffolding

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updated 12.9 years ago by Richard Smith-Unna

• written 14.6 years ago by Luke

Just curious - why not MIRA?

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written 14.5 years ago by Gaffa

1 answer

I would try using SSPACE and GapFiller in that order.

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

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updated 7.5 years ago by Ram

• written 12.9 years ago by Richard Smith-Unna

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