[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 8 Sep 2009 09:51:57 +0200
OK, so finally MIRA completed with the combined 454/Solexa data run.
Here is the call parameters & info:
mira -project=M1 -job=denovo,genome,normal,454,solexa
-GENERAL:number_of_threads=4 SOLEXA_SETTINGS -CO:msr=no
-GE:uti=no:tismin=2000:tismax=3000
Localtime: Mon Sep 7 12:46:26 2009
Assembly information:
=====================
Num. reads assembled: 3392921
Num. singlets: 33
Large contigs:
--------------
With Contig size >= 500
AND (Total avg. Cov >= 20
OR Cov(san) >= 0
OR Cov(454) >= 13
OR Cov(sxa) >= 6
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 1066
Total consensus: 3770477
Largest contig: 306903
N50 contig size: 117364
N90 contig size: 802
N95 contig size: 638
Coverage assessment:
--------------------
Max coverage (total): 2110
Max coverage
Sanger: 0
454: 241
Solexa: 2005
Solid: 0
Avg. total coverage (size >= 5000): 58.56
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 39.42
Solexa: 18.93
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 22
Consensus bases with IUPAC (IUPc): 634 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 5 (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: 50303
Total consensus: 6877147
Largest contig: 306903
N50 contig size: 757
N90 contig size: 35
N95 contig size: 31
Coverage assessment:
--------------------
Max coverage (total): 2546
Max coverage
Sanger: 0
454: 241
Solexa: 2548
Solid: 0
Avg. total coverage (size >= 5000): 58.56
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 39.42
Solexa: 18.93
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 18
Consensus bases with IUPAC (IUPc): 2382 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 5 (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)
I find the result is more messy that the ~70 contigs from the 454-data only
assembly. The longest contigs are a bit longer, but none of the big contigs
appear to have been joined. And then a fair number of short contigs have
appeared.
Bwt. I did check the integrity of the Solexa mate pair data and it does look
OK.
Martin
On Fri, Sep 4, 2009 at 9:15 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Freitag 04 September 2009 Martin A. Hansen wrote:
> > Btw, I have a feeling that the preparation of the mate-pair library was
> > somehow was faulty so that there are no mate-pair reads - only single
> > reads. Would that effect run-time of MIRA?
>
> Using templates has some impact of O(nlog(n)) with n being number of
> paired-
> end reads in contig during contig assembly. Should not be too noticable
> unless
> one has contigs with a million reads or more.
>
> Hmmm ... which may be the case for hybrid assemblies. I'll have to rethink
> whether trading space for time is needed.
>
> Regards,
> Bastien
>
>
>
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