Reference Based de Novo Assembly

[Fernando Seixas]

Hi,

I'm trying to de novo assembly the genome of a non-model mammalian species with a relatively large genome (~3 Gb) for which we have a relatively close reference - average 5% divergent (~12 My). What I was wondering is if there is any way I can take advantage of this relatively close reference to assemble my genome and in that case what would be the best strategy.

One of things I thougth was to first do the de novo assembly of my genome (in allpaths-lg, for which the data was specially tailored) and then to use the reference to help scaffolding the contigs/scaffolds resulting from the de novo assembly - i'm aware that, for instance, AlignGraph is designed for this task. Could this be a good solution or is there any other tool available (not that I don't want to use AlignGraph but I want to be aware of the possible tools)?

Thanks,
Fernando

[illinu]

You can still use ALLPATHS-LG with the reference based assembly option

[syfo]

I'm curious about this one: IDBA-Hybrid: an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing

[illinu]

Let us know how it goes. I guess by hybrid it means short reads and PacBio??
I used a very close reference (2 My) to aid a de novo assembly with ALLPATHS-LG and I saw no improvement over the de novo itself. Plus I am not sure it is a good idea to force DNA to go where your close reference has it, the little difference between the two species might be due to gene copy, larger genes or in different places of the genome. I am not too keen to use a reference if it's not the same species. For scaffolding it is a good idea. Have you tried SSPACE? you can also use a transcriptome to scaffold.

[EricSchon]

Hi I am considering using AlignGraph as well to improve my de novo assembly (only PE illumine reads) of a filamentous fungus (30 Mb genome). What was your experience with the tool?

[ymc]

I want to assemble a bacteria strain from only PE150 reads. I have a finished reference that is the same lineage of the strain. I already mapped my reads to the reference and generated a bam.

Which reference-based assembler do you recommend for my case? Thanks a lot!

[illinu]

You have a lot of options but for bacteria look at MIRA, Ray, Abyss, Velvet... I find that depending on the species one software might perform better than other so you have to try several and see which one works best for you.