Assemble genomes from different sequencing platforms

Question

[Elizabeth]

Is it possible to combine two assemblies from two different sequencing platforms ? If yes, what are the names of some of the softwares that does that? I have read about Ray, but I'm not sure if it can perform this function. The goal here is to make larger contigs/supercontigs with minimal gaps. Thank you.

[cschu181]

What are the sequencing platforms in question? Some assemblers (e.g. unicycler for bacterial/microbial data) can take reads from different sources as input, e.g. for scaffolding.

[Elizabeth]

It's a eukaryotic genome. I have assembled it separately. The question is whether I can take this already assembled genome and combine it to create a more complete version of the genome. The platforms are 454 and Illumina.

Answer 1

[JC]

Some assemblers allow you to combine techs as pointed before (Mira assembler for example), but answering your question, yes, it's valid to combine the contigs or scaffolds, just be aware that error rate is different between technologies and some variations could occur when you compare your sequences from one assembly to the other.

Answer 2

[Damian Kao]

I've used GAM-NGS in the past with some success:

https://github.com/vice87/gam-ngs