[mira_talk] Re: Assembling 454 with mira3
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 2 Jul 2010 19:33:10 +0200
On Freitag 02 Juli 2010 Philip Stevens wrote:
> i am little dissapointed cause my sequencer told me that the propability to
> get the fastq or sff files of my sequencing is very low.
With all due respect towards your sequencer ... but this is an unacceptable
answer. At least it would be for me. Search another provider ASAP.
> So i will need
> some help to get best results with fasta only sequencing.
>
> here is my position:
>
> i have about 32k 454 Reads to assemble but dont have any fastq or sff
> files. So what are best parameters?
The following has no guarantee, I never assemble without qualities.
Find out the theoretical coverage of your genome. Then use
--project=CBS -job=denovo,genome,accurate,454 --fasta --noqualities
-CL:pec=30
454_SETTINGS
-AS:bdq=30
-CO:fnicpst=yes:mrpg=...
where for -CO:mrpg=... you insert 1/3 of the theoretical coverage.
The result will be really suboptimal though.
Furthermore I hope your genome is not larger than 300k, else you'll get
problems with coverage.
B.
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