[mira_talk] contigs built only by one sequence
- From: Laurent Manchon <lmanchon@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Dec 2009 22:30:16 +0100
--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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