SeqMan NGen Denovo genome sequencing

[naragam]

Hello! I'm just starting to use Denovo genome assembly using SeqMan NGen for looking at some reads from a 454 sequencer. The samples are from a mixed strain population of Plasmodium falciparum containing 3d7, HB3, K1, RO33, and other strains. Our previous analysis using a homegrown pipeline using ShoRAH and some in-house developed s/w for clustering has failed to show the correct frequencies of the strains in the mixture. So we are attempting to assemble the generated sequences from 454 using Denovo genome assembly in SeqMan NGen.

Here are my beginner's questions-

1. How do we force assembly of haplotypes w/o necessarily resorting to BAM format output? But SeqMan NGen won't allow that option w/o BAM format?

2. How do we make use of the plethora of Advanced Assembly options in SeqMan NGen?

3. How do we control very low frequency haps from getting collapsed into SNP contigs, but keep them as separate contigs?

4. If someone has some guidelines to use in the setting of parameters can you please share them with us?

Thanks much,

Nash