[mira_talk] assembly options for non-redundant contigs

  • From: Richard Gregory <R.Gregory@xxxxxxxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Tue, 02 Jun 2009 17:30:23 +0100

Hi All,

We been using Mira for a while now, handles cDNA much better than Newbler and gives us more confidence in the result.

The latest batch of data is proving to be a problem, the current project requires contigs that contain all similar reads and not be split into multiple contigs of minor (or maybe large) differences. We are having trouble finding the options to achieve this. Does anybody know if/how this can be done?

The sequence data is 1.5 plates of 454 Titanium cDNA and half a plate of pre-Titanium cDNA. Have tried many options, genome or est, --noclippings, -SK:mmhr=1, -DP:ure=no, -AS:ard=no, -AL:egp=no, -AS:sd=no, -CO:mr=no, -AL:mrs=55, -SK:mnr=yes, -SK:hss=1:pr=70, but the result is basically the same. The better option set was -fasta -job=denovo,est,draft,454 --noclippings -SK:mmhr=1 -DP:ure=no -AS:ard=no -AS:sd=no -GE:not=4 -SK:hss=1:pr=70 , but this was marginally better and doesn't achieve the desired result.

The only clue comes previous assemblies with earlier versions of Mira, which produced much less redundancy, ie, was ~8000 contigs, now V2.9.43 produces ~18000. Mapping this onto a reference showed ~1500 contigs could be the same gene. Assembling the ~1500 contigs with cap3 produced ~3 contigs, one containing hundreds of contigs.



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