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

  • From: Martin Mokrejs <mmokrejs@xxxxxxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sat, 08 Oct 2011 13:21:44 +0200

Hi,
  can you show the 454 adaptor sequence you searched for? Along with
some input 20 entries in FASTA format before and after that "masking"?
Finally, send "sffinfo -s -n" for those first 20 entries? Maybe you failed
to mask the adaptors? Or to send it to me directly so that we do not spoil
the email list if you cannot upload it to some public place.

Did you try just 454 data assembly alone?
Martin

Hui Sun 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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