[mira_talk] Re: Annotation Pipelines
- From: Francisco Pina Martins <f.pinamartins@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 7 Oct 2013 19:33:34 +0100
It can help you to automate and organize BLAST results. But I am really not
sure if that's what you need...
Em 07/10/2013 19:21, "Adrian Pelin" <apelin20@xxxxxxxxx> escreveu:
> I am a bit confused about what it actually does. Says it's for NGS data
> analysis. What type of data analysis. Variant detection, that's just
> finding SNPs and genotypes.
>
> What about annotating the genome? Gene prediction?
> Adrian
>
> On 10/7/2013 2:02 PM, Francisco Pina Martins wrote:
>
> https://github.com/StuntsPT/4Pipe4
>
> Forgot the link...
> Em 07/10/2013 19:01, "Francisco Pina Martins" <f.pinamartins@xxxxxxxxx>
> escreveu:
>
>> Sorry to be advertising my own program, but you may be interested in
>> 4pipe4.
>> It is meant for variant detection, but you can tweak it slightly for
>> other kinds of annotations...
>> Hope this might be of help.
>> Em 07/10/2013 18:51, "John Nash" <john.he.nash@xxxxxxxxx> escreveu:
>>
>>> I'm not sure on its abilities to work with eukaryotes. I'm sorry, I
>>> live in a prokaryotic research world and should have specified the Kingdom
>>> - that slipped my mind.
>>>
>>> J
>>>
>>> On 2013-10-07, at 1:45 PM, Adrian Pelin wrote:
>>>
>>> would it detect introns based on AA seqs of close relatives?
>>>
>>>
>>> On Mon, Oct 7, 2013 at 1:42 PM, John Nash <john.he.nash@xxxxxxxxx>wrote:
>>>
>>>>
>>>> On 2013-10-07, at 1:36 PM, Adrian Pelin wrote:
>>>>
>>>> I was wondering if anyone had an automatic annotation pipeline of
>>>> choice that they apply on MIRA assemblies?
>>>>
>>>> I tried to use MAKER online, it doesn't really work anymore. Any
>>>> thoughts?
>>>>
>>>> --
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>>>>
>>>>
>>>> I use PROKKA - http://www.vicbioinformatics.com/software.prokka.shtml
>>>>
>>>> It's awesome but a bit of an ordeal to install. Torsten (the author)
>>>> is another prokaryote genome rock star, and his work should be followed as
>>>> he write useful tools.
>>>>
>>>> John
>>>>
>>>> --
>>>> John HE Nash, PhD
>>>> Research Scientist
>>>> Division of Science & Technology
>>>> Laboratory for Foodborne Zoonoses
>>>> Public Health Agency of Canada.
>>>>
>>>> 110 Stone Road West, Guelph, ON, N1G 3W4 (Tuesdays & Wednesdays)
>>>> 180 Queen St West, #11-103A (11th Floor), Toronto, ON, M5V 3L9 (RoW)
>>>>
>>>> Adjunct Professor, Department of Pathobiology, Ontario Veterinary
>>>> College, University of Guelph.
>>>>
>>>>
>>>
>>> --
>>> John HE Nash, PhD
>>> Research Scientist
>>> Division of Science & Technology
>>> Laboratory for Foodborne Zoonoses
>>> Public Health Agency of Canada.
>>>
>>> 110 Stone Road West, Guelph, ON, N1G 3W4 (Tuesdays & Wednesdays)
>>> 180 Queen St West, #11-103A (11th Floor), Toronto, ON, M5V 3L9 (RoW)
>>>
>>> Adjunct Professor, Department of Pathobiology, Ontario Veterinary
>>> College, University of Guelph.
>>>
>>>
>
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