[mira_talk] Re: contigs built only by one sequence

  • From: Laurent Manchon <lmanchon@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sun, 10 Jan 2010 21:44:25 +0100

Bastien Chevreux a écrit :
On Donnerstag 07 Januar 2010 Laurent MANCHON wrote:
okay by adding parameter -OUT:sssip=no the singlets are not saved in the
assembly result.
so the command line syntax is (v2.9.43):

Please note that 2.9.43 is one of the last versions which had misasembly problems in some cases and that you should use a newer version.

Regards,
  Bastien

yes i'm agree with you but i have some problems to find the corresponding and good command line syntax in the current version (mira3rc4d)
can you help me ?

on v2.9.43 is :

bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454 
-OUT:sssip=no -notraceinfo  \
-GENERAL:kcim=yes,not=3 -SK:rt=4 \
-CO:fnicpst=yes,rodirs=10,asir=yes,mr=no \
-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

Laurent --




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