[mira_talk] Re: contigs built only by one sequence
- From: "Yi Zheng" <yz357@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Dec 2009 22:10:53 -0500 (EST)
Hi Laurent,
From the list I know your also use mira2.9.43 like me. I have a 64-bit
version of mira2.9.43, but now I need a 32-bit version run on server. If
you have one. can you sent it to me! Thank you so much.
I know your problem, if the id of contig have a 's' like 'mira_s123', this
contig was from one sequence. So I think you can remove this part of
contigs from you assembly result.
Now the new version of mira3rc4 has fix this problem. you can also use the
new one.
> --Hi,
>
> i have made assembly on 454 reads (~600 000 reads) using mira 2.9.43 and
> with this command line:
>
> bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454
> -notraceinfo -GENERAL:kcim=yes,not=3 -SK:rt=4
> -CO:fnicpst=yes,rodirs=10,asir=yes
> -CL:cpat=no,pec=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc=yes,mrcr=0,smrc=0
> -AL:bip=5,bmin=10,mrs=90:egp=yes:egpl=reject_codongaps:megpp=100,mo=60
> -AS:mrl=30,bdq=30 -SK:mnr=yes,rt=8,mmhr=6
>
> and i obtain 53867 contigs but some contigs (~18163) are only built
> using one sequence, why ?
> So, i don't understand...
> I thought that contigs established(constituted) by a single sequence was
> singulets and had to appear in debrislists, don't you ?
>
> Laurent --
>
>
> planaire_info_assembly.txt file :
>
> Assembly information:
> =====================
>
> Num. reads assembled: 469768
> Num. singlets: 18163
>
> Large contigs:
> --------------
> With Contig size >= 500
> AND (Total avg. Cov >= 5
> OR Cov(san) >= 0
> OR Cov(454) >= 5
> OR Cov(sxa) >= 0
> OR Cov(sid) >= 0
> )
>
> Length assessment:
> ------------------
> Number of contigs: 6322
> Total consensus: 6868966
> Largest contig: 7814
> N50 contig size: 1170
> N90 contig size: 701
> N95 contig size: 614
>
> Coverage assessment:
> --------------------
> Max coverage (total): 2681
> Max coverage
> Sanger: 0
> 454: 4285
> Solexa: 0
> Solid: 0
> Avg. total coverage (size >= 5000): 14.27
> Avg. coverage (contig size >= 5000)
> Sanger: 0.00
> 454: 14.27
> Solexa: 0.00
> Solid: 0.00
>
> Quality assessment:
> -------------------
> Average consensus quality: 19
> Consensus bases with IUPAC (IUPc): 11449 (you might want
> to check these)
> Strong unresolved repeat positions (SRMc): 73 (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: 35715
> Total consensus: 30892000
> Largest contig: 7814
> N50 contig size: 681
> N90 contig size: 349
> N95 contig size: 283
>
> Coverage assessment:
> --------------------
> Max coverage (total): 2681
> Max coverage
> Sanger: 0
> 454: 4285
> Solexa: 0
> Solid: 0
> Avg. total coverage (size >= 5000): 14.27
> Avg. coverage (contig size >= 5000)
> Sanger: 0.00
> 454: 14.27
> Solexa: 0.00
> Solid: 0.00
>
> Quality assessment:
> -------------------
> Average consensus quality: 11
> Consensus bases with IUPAC (IUPc): 53965 (you might want
> to check these)
> Strong unresolved repeat positions (SRMc): 73 (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)
>
>
>
>
>
> --
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