[mira_talk] Re: Denovo hybrid assembly of a 3.8M genome using 454 and Solexa

  • From: John Nash <john.he.nash@xxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Fri, 7 Oct 2011 18:33:44 -0400

Your stats look like it was not a subset. 

J

Sent from my mobile device

On 2011-10-07, at 5:23 PM, Hui Sun <hsun@xxxxxxx> wrote:

> Hello,
> 
> I am trying to assemble a genome with an estimated size of 3.8M.  I
> have used allpath and generated an assembly.  As a comparison, I'm
> trying to use MIRA assembler.
> 
> I have 4 million 454 PE reads and 120 million Solexa reads. I have
> screened out adaptors by using SSAHA2.
> 
> I then subset Solexa reads to 2.5 million and 454 reads to 400K, which
> is ~42x coverage for each of the platform. I then ran MIRA hybrid
> denovo assembly: mira
>  --project=test --job=denovo,genome,normal,454,solexa
> 
> The resulting contig stats seem to be really fragmented, see stats
> below.  What can I do to improve scaffolding?   My allpath assembly
> generated 15106 contigs, 11965 scaffolds, N50 contig size 1.9kb, which
> seems to be much better.  Thanks for the help.
> 
> All contigs:
> ============
>  Length assessment:
>  ------------------
>  Number of contigs:    124259
>  Total consensus:    46425879
>  Largest contig:    4936
>  N50 contig size:    402
>  N90 contig size:    240
>  N95 contig size:    206
> 
>  Coverage assessment:
>  --------------------
>  Max coverage (total):    298
>  Max coverage per sequencing technology
>    Sanger:    0
>    454:    304
>    IonTor:    0
>    PacBio:    0
>    Solexa:    767
>    Solid:    0
> 
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