[mira_talk] Re: one strain assembles better than a second similar strain?

  • From: Adam Witney <awitney@xxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 20 Oct 2011 22:20:54 +0100

thanks for your replay, replies below.

> Anyway, there are a couple of clues in the information you posted: the 
> coverage information. "Large contigs" in both strains have a coverage of 
> ~20x, yet the first strain has a contig with a max coverage of 680x, while 
> the other strain (the one with the longer assembly time) has a contig with 
> max coverage of 790x.
> 
> In both cases the fold difference of 34 to 39 (ration between 20x and 
> 680x/790x) is a lot higher than I am used from "normal" bacteria, that would 
> be my first angle of attack: what are these high coverage contigs, why does 
> one strain seem to have a couple more than the other.

ah ok, so the 793 contig looks to be just repetitive junk, from contigstats:

PA128572_316_1_c1311    1236    23      1378    793     122.73  49.11   4       
0       0       0       59      0       
PA128572_316_1_rep_c1395        2024    60      1350    108     73.68   65.42   
0       0       0       0       11      0

the next contig down in size has a max coverage of only 108

> Second thing to look at: kmer repeat histogram (hash statistics) which you 
> did not post but can tell you quite a bit.

I'm not sure where I would find this information?

> Third thing: after the hash statistics, have a look at the read repeat info 
> file, and there specially the stretches tagged MNRr. They can be quite 
> informative regarding either sequencing artefacts (some kind of adaptor not 
> clipped) or really high copy number stretches.

the readrepeats file contains 4729 MNRr out of 6548 rows, I can't see any 
particular pattern though

thanks again

adam


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