[mira_talk] Re: Denovo assembly of a high GC bacteria
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 22 Mar 2010 08:45:30 +0100
Better, but not a lot ...
Martin
mira -project=achro -job=denovo,genome,normal,454 454_SETTINGS -CO:mrpg=20
Localtime: Sat Mar 20 18:41:53 2010
Assembly information:
=====================
Num. reads assembled: 1932597
Num. singlets: 434
Large contigs:
--------------
With Contig size >= 500
AND (Total avg. Cov >= 33
OR Cov(san) >= 0
OR Cov(454) >= 33
OR Cov(sxa) >= 0
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 385
Total consensus: 7002837
Largest contig: 152999
N50 contig size: 39654
N90 contig size: 9779
N95 contig size: 6190
Coverage assessment:
--------------------
Max coverage (total): 792
Max coverage
Sanger: 0
454: 969
Solexa: 0
Solid: 0
Avg. total coverage (size >= 5000): 99.51
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 100.03
Solexa: 0.00
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 86
Consensus bases with IUPAC (IUPc): 25 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 1 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
All contigs:
------------
Length assessment:
------------------
Number of contigs: 3127
Total consensus: 8539945
Largest contig: 152999
N50 contig size: 32126
N90 contig size: 614
N95 contig size: 430
Coverage assessment:
--------------------
Max coverage (total): 792
Max coverage
Sanger: 0
454: 969
Solexa: 0
Solid: 0
Avg. total coverage (size >= 5000): 99.00
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 99.82
Solexa: 0.00
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 38
Consensus bases with IUPAC (IUPc): 453 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 1 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
On Thu, Mar 18, 2010 at 9:34 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Donnerstag 18 März 2010 Martin A. Hansen wrote:
> > I have 2M 454 titanium reads (~500bp in length). GC content is 65% (!)
> and
> > genome size is 7Mb.
> >
> > I have a fairly good assembly done with Newbler:
> > [...]
> > So I wanted to do an assembly with Mira to compare the assemblies. I
> > followed the Mira 454 tutorial (sff_extract and remembering to include
> > quality and traceinfo!) and simply ran with the following options:
> > [...]
> > But the result is disappointing:
> > So, any suggestions?
>
> I suppose the standard config does not cope very well with high coverages
> as
> you have (~100x), it's is geared towards more 'normal' coverage. I suppose
> that this together with the high GC will lead to many false positive
> repeats
> detected.
>
> Hmmm ... could you please try adding
> 454_SETTINGS -CO:mrpg=20
>
> and tell whether this improves the assembly?
>
> Regards,
> Bastien
>
>
>
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