non-trivial de novo assembly - what to use?

[yaximik]

Hi all,

I am looking for a tool for a difficult task - de novo assembly of a mammalian size genome from Illumina/454 shotgun reads using degraded ancient DNA without using a reference. This means no mate pairs as DNA fragments, paired ends (in Illumina's sense) at best. What would be the best choice of a de novo assembler?

[flxlex]

Oh dear... Hybrid assembly with 454 and Illumina is anyway a difficult task. If your Illumina reads are 150 bp or longer, you may try newbler. But Celera would be my best bet - although it is demanding to get the hang of it.

[yaximik]

Well, I guess I did not express this right. Mostly Illumina reads. Considering lack of opportunity using mate pairs, I guess I should try get as long reads as the sample allows. 454 gets involved primarily because of the longest reads. Bioanalyzer shows that DNA still has some long fragments as smear extends above 1000 bp marker (perhaps RNA chip would be more adequate though). Anyway, the idea is to avoid using reference human genome as much as possible as this may lead to loss of what is really different.