Re: [Mauve-users] SNPs finder - draft and complete genomes

[Walter, M. <ma...@wa...>]

Hi Cristina,

sorry, I better had answered to the Mauve mailing list.

Indeed, you can perform the alignment with many drafts and as long as you
just want to extract the SNPs afterwards, it does not matter, if the
contigs are ordered or not. But just in case you will look for genome
rearrangements or if some SNPs are located in a coding region, I recommend
ordering the contigs before.

I also recommend ordering just one draft genome using the GUI and than
running the remaining reorderings at the command line in a loop. You can
just copy the corresponding command from the log window and adapt it.

--
Regards,
Mathias

2016-08-17 13:26 GMT+02:00 Cristina Kraemer Zimpel <cri...@gm...>:

> Hi Mathias, thank you for the tips.
> If you allow me, I would like to ask another question.
> Can I perform multiple alignment with many drafts? Or should I reorder the
> contigs one at time with the reference and look for gap closure to perform
> the multiple alignment?
>
>
> Thank you again
>
>
> 2016-08-17 2:22 GMT-03:00 Walter, Mathias <ma...@wa...>:
>
>> Hi Cristina,
>>
>>
>> reordering of the contigs is always a good idea. Additionally, I usually
>> rotate it to move the oriC to the start of the linearized chromosome. That
>> makes visual inspection much easier. The contig mover produces 1 to n
>> folders named alignment1 to alignmentN and put the reordered contigs into a
>> fasta file having the same name as you original file. For tracing the
>> reorder process, you can look at the tab file.
>>
>> Be carefull with reference-based SNP coordinates. Sometimes they are
>> increases by one in the middle of the genome. I used ParSNP (
>> https://github.com/marbl/parsnp) to circumvent this. It can read the
>> XMFA files produced by Mauve.
>>
>> --
>> Regards,
>> Mathias
>>
>> 2016-08-17 1:16 GMT+02:00 Cristina Kraemer Zimpel <cri...@gm...>
>> :
>>
>>> Greetings
>>> I intend to align genomes of Mycobacterium strains in order to find SNPs
>>> using MAUVE. Few genomes are complete and few are draft.
>>>
>>> For the draft genomes. Should I reorder the contigs with the reference:?
>>> And which output file after reorder contigs should I use for the
>>> comparison with complete genomes.
>>> Thank you
>>> Best regards.
>>>
>>> --
>>> Cristina Kraemer Zimpel
>>>
>>> Médica Veterinária, Especialista em Medicina Veterinária do Coletivo
>>> Mestranda em Epidemiologia Experimental Aplicada às Zoonoses
>>>
>>> Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS),
>>> FMVZ - USP
>>> Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária
>>> São Paulo, SP, CEP 05508 270, Brasil
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>>
>>> _______________________________________________
>>> Mauve-users mailing list
>>> Mau...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mauve-users
>>>
>>>
>>
>
>
> --
> Cristina Kraemer Zimpel
>
> Médica Veterinária, Especialista em Medicina Veterinária do Coletivo
> Mestranda em Epidemiologia Experimental Aplicada às Zoonoses
>
> Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS), FMVZ
> - USP
> Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária
> São Paulo, SP, CEP 05508 270, Brasil
>
>