[mira_talk] Re: (no subject)
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 22 Jul 2014 21:50:49 -0500
If you are using Mira in mapping mode, it will only give you as many contigs as
your reference has. So if your reference is a single contig assembly, Mira will
map the reads and give back a single contig. In addition, since Mira knows how
to handle multiple strains, you can get a consensus that has each strain
individually, as well as a consensus that uses all the strains. So depending on
what information you want to get, you can use one or the other (or both). Mira
also has a handy feature for calling SNPs based on the mapping to the reference
(see miraconvert -t hsnp).
Velvet, as far as I know, does not do mapping assemblies. It only does denovo
assemblies, so you will definitely get more contigs. You can run Mira in denovo
mode to do the same thing, it just depends on what you are trying to get out of
your data.
> On Jul 22, 2014, at 7:17 PM, "Mendez Garcia, Celia" <cmendezg@xxxxxxxxxxxx>
> wrote:
>
> Hello Bastien,
>
> thanks. It worked by re-trying. 256 GB is the amount of memory I'm using.
> Just 1 CPU core...
>
> Another tiny tiny thing: I'm mapping several genomes against a reference and
> always get just one contig. My supervisor asks how come. What should I reply
> to this, I mean, is this usual? This is basically good news, but I guess
> most people here use Newbler for 454 and Velvet for Illumina data and you
> don't get this using those that easily [actually we've been using Velvet for
> this and getting ~200 contigs for what MIRA got 1].
>
> Thanks again.
>
> Celia
> From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] on
> behalf of Bastien Chevreux [bach@xxxxxxxxxxxx]
> Sent: Friday, July 18, 2014 6:11 PM
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: (no subject)
>
> Yeah, right ... and your mail *was* to MIRA talk. Looks like I confused a
> couple of things, sorry :-)
>
>> On July 18, 2014 at 12:24 AM "Mendez Garcia, Celia" <cmendezg@xxxxxxxxxxxx>
>> wrote:
>>
>> Hi,
>>
>> I get this log file when mapping to a reference bacterial genome.
>> What's the problem here?
>>
>> Thanks,
>> Celia
>
>
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