[mira_talk] Re: --highlyrepetitive vs normal
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 13 Oct 2012 14:22:02 +0200
On Oct 11, 2012, at 18:43 , Juan Daniel Montenegro Cabrera wrote:
> [...]
> and the Y axis is the result of adding the --highlyrepetitive flag.
>
> The assemblies are quite similar, but for some reason there is one huge
> missassembly in the first reference contig. The mira manual does not say much
> about the flag and I wanted to know what are the exact changes of this flag
> in the assembly process.
The changes by "highlyrepetitive" are quite varied. Once encountered, a whole
set of standard parameters is changed by default and some are dynamically
adjusted. First the default settings applied:
"\n_COMMON_SETTINGS"
"\n\t-AS:sep=yes"
"\n\t-CO:mr=yes:mroir=false"
"\n\t-SK:mnr=yes:nrr=10"
"\n"
"\n_SANGER_SETTINGS"
"\n\t-GE:uti=yes"
"\n\t-AS:urdcm=1.2"
"\n\t-CL:pvlc=yes:pvcmla=10"
"\n\t-DP:ure=yes:feip=0:leip=0"
"\n\t-CO:emea=15:amgb=yes:amgbemc=yes:amgbnbs=yes"
"\n"
"\n_454_SETTINGS"
"\n\t-DP:ure=no"
"\n\t-AS:urdcm=1.4"
"\n\t-CL:pvlc=yes:pvcmla=10"
"\n\t-CO:emea=5:amgb=no"
"\n"
// TODO: what for IonTorrent? atm like 454
"\n_IONTOR_SETTINGS"
"\n\t-DP:ure=no"
"\n\t-AS:urdcm=1.4"
"\n\t-CL:pvlc=yes:pvcmla=10"
"\n\t-CO:emea=5:amgb=no"
"\n"
"\n_PCBIOHQ_SETTINGS"
"\n\t-DP:ure=no"
"\n\t-AS:urdcm=1.4"
"\n\t-CL:pvlc=yes:pvcmla=10"
"\n\t-AL:egp=no"
"\n\t-CO:emea=5:amgb=no"
"\n"
// TODO: PacBio LQ
"\n_PCBIOLQ_SETTINGS"
"\n\t-DP:ure=no"
"\n\t-AS:urdcm=1.4"
"\n\t-CL:pvlc=yes:pvcmla=10"
"\n\t-AL:egp=no"
"\n\t-CO:emea=5:amgb=no"
"\n"
"\n_SOLEXA_SETTINGS"
"\n\t-DP:ure=no"
"\n\t-AS:urdcm=1.9"
"\n\t-CL:pvlc=no"
"\n\t-CO:emea=5:amgb=yes:amgbemc=yes:amgbnbs=yes"
// for Text "technology", nothing
After that, -AS:nop and -AS:rbl are adjusted, the code and output should speak
for itself:
if(tmpactpar->mp_assembly_params.as_numpasses<6){
cout << " - increassing number of passes (-AS:nop) ";
tmpactpar->mp_assembly_params.as_numpasses++;
if(tmpactpar->mp_assembly_params.as_numpasses<=5){
tmpactpar->mp_assembly_params.as_numpasses++;
cout << "by two.\n";
}else{
cout << "by one.\n";
}
}
if(tmpactpar->mp_assembly_params.as_numrmbbreakloops<3){
cout << " - increasing maximum of RMB break loop (-AS:rbl).\n";
tmpactpar->mp_assembly_params.as_numrmbbreakloops++;
}
B.
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