Multiple libraries of different lengths - single or seperate assemblies?

[samche42]

Hi!

I have three Ion torrent libraries; a 600bp, 400bp and a 200bp library. I intend to use SPAdes to assemble the reads into contigs but am unsure whether I can use three different sized libraries in a single assembly? (As I'm pretty sure it's going to have an affect on the optimal k-mer value).

Has anyone used various read sizes in a single assembly or would it be wiser to assemble one library at a time and use the resultant contigs from the first assembly as "untrusted contigs" in the next assembly and so on?

Any advice would be massively appreciated!!

[Brian Bushnell]

SPAdes documentation seems to indicate that the distribution of insert size is important to some of its heuristics, but I think coverage is more important... also it's a multi-kmer assembler so you don't need a single ideal kmer length. I normally run with K=25,55,95,125. I'd just feed them all into SPAdes.

[samche42]

Ok brilliant - Thanks Brian