[mira_talk] Re: contigs built only by one sequence

  • From: Laurent Manchon <lmanchon@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 18 Dec 2009 08:27:03 +0100

Yi Zheng a écrit :

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.


yes i think i have a 32-bit version of mira2.9.43
but until january i will not at my office, if you can wait january...

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.
yes but in version mira3rc4 i have not yet found the analog command to obtain the same result. 

thank you,
laurent --

--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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