Hello - Anyone ever used Geneious?!

jeremyrualosr · 03-23-2011, 05:47 PM

New to SeqAnswers so hello...? Found some posts about Geneious and they said something about having server capabilities with Bowtie, Maq and it's own assembler...

Any Thoughts?

Cheers

ECO · 03-23-2011, 06:54 PM

Welcome Jeremy,

I'm going to guess that your post will get more eyes in the Bioinformatics forum...so I'm moving it there.

shandley · 03-24-2011, 06:25 AM

I have a full license to Geneious. It is a great (arguably the best all-inclusive) genomics and phylogenetics package on the market.

That being said, it is relatively costly and you can accomplish much (if not all) of what it does using free software. That's how it always goes with pay vs. free software.

So I would say it really is more of a fiscal issue than a technical one.

Specifically for your alignment question I have actually never used Geneious for this. I prefer the command line which allows for much more rapid paramater changing and piping.

Feel free to email me if you have any specific questions.

SAH

Milkman · 03-24-2011, 07:11 PM

Hi Jeremy

I began using Geneious Pro last year when I began work on an Illumina GE machine. I had minimal bioinformatics experience other than alignments and trees. I found it easy to use for de novo assembly of contigs and to batch blast them. It gave me nice graphics that I have used in several publications that arose from the work. Most of what it does is freely available as command line programs, but it does most of what I need in the one package. I use an iMac and it runs well on their Snow Leopard OS.

It is probably not right for you if you are a whiz with perl and unix but for the biologist who is thrown in the deep end with 40 million reads to analyse, I highly recommend it.

Pedro · 03-25-2011, 05:46 PM

Hi,

I have a Geneious license and before deciding which integrated solution I would select, I tested also CLC Genomics, DNAstar, and NextGene solutions. Among all I decided for Geneious. Nonetheless, I do expect some improvements in the next release (which should be soon). For instance, I am not very happy with their ngs assembler and in fact I dedicated part of my time learning linux basics to use several free bioinfo tools. In my opinion (although I'm a biologist) is not so difficult to "compile/use" many of the available tools which gives very high quality results.(in other cases you run into hard successive errors...ouch).
In sum, I would advise Geneious however, at a certain point you might find important/crucial to explore/learn other tools

jeremyrualosr · 04-07-2011, 08:57 PM

I keep hearing that... that everyone basically loves Geneious but they have to learn how to use the freeware either way... I believe Geneious has Bowtie in it and a Geneious Server that can run NGS stuff on clusters... well, thanks for the feedback!

JaRu

Quote:

Originally Posted by Pedro

Hi,

I have a Geneious license and before deciding which integrated solution I would select, I tested also CLC Genomics, DNAstar, and NextGene solutions. Among all I decided for Geneious. Nonetheless, I do expect some improvements in the next release (which should be soon). For instance, I am not very happy with their ngs assembler and in fact I dedicated part of my time learning linux basics to use several free bioinfo tools. In my opinion (although I'm a biologist) is not so difficult to "compile/use" many of the available tools which gives very high quality results.(in other cases you run into hard successive errors...ouch).
In sum, I would advise Geneious however, at a certain point you might find important/crucial to explore/learn other tools

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03-23-2011, 05:47 PM	#1
jeremyrualosr Junior Member Location: Baltimore, MD Join Date: Mar 2011 Posts: 3	Hello - Anyone ever used Geneious?! New to SeqAnswers so hello...? Found some posts about Geneious and they said something about having server capabilities with Bowtie, Maq and it's own assembler... Any Thoughts? Cheers

03-24-2011, 07:11 PM	#4
Milkman Junior Member Location: Australia Join Date: Feb 2011 Posts: 3	Geneious Hi Jeremy I began using Geneious Pro last year when I began work on an Illumina GE machine. I had minimal bioinformatics experience other than alignments and trees. I found it easy to use for de novo assembly of contigs and to batch blast them. It gave me nice graphics that I have used in several publications that arose from the work. Most of what it does is freely available as command line programs, but it does most of what I need in the one package. I use an iMac and it runs well on their Snow Leopard OS. It is probably not right for you if you are a whiz with perl and unix but for the biologist who is thrown in the deep end with 40 million reads to analyse, I highly recommend it.

03-23-2011, 06:54 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Welcome Jeremy, I'm going to guess that your post will get more eyes in the Bioinformatics forum...so I'm moving it there.

03-24-2011, 06:25 AM	#3
shandley Member Location: Saint Louis, MO Join Date: Sep 2010 Posts: 58	I have a full license to Geneious. It is a great (arguably the best all-inclusive) genomics and phylogenetics package on the market. That being said, it is relatively costly and you can accomplish much (if not all) of what it does using free software. That's how it always goes with pay vs. free software. So I would say it really is more of a fiscal issue than a technical one. Specifically for your alignment question I have actually never used Geneious for this. I prefer the command line which allows for much more rapid paramater changing and piping. Feel free to email me if you have any specific questions. SAH

03-25-2011, 05:46 PM	#5
Pedro Junior Member Location: Portugal Join Date: Dec 2008 Posts: 6	Hi, I have a Geneious license and before deciding which integrated solution I would select, I tested also CLC Genomics, DNAstar, and NextGene solutions. Among all I decided for Geneious. Nonetheless, I do expect some improvements in the next release (which should be soon). For instance, I am not very happy with their ngs assembler and in fact I dedicated part of my time learning linux basics to use several free bioinfo tools. In my opinion (although I'm a biologist) is not so difficult to "compile/use" many of the available tools which gives very high quality results.(in other cases you run into hard successive errors...ouch). In sum, I would advise Geneious however, at a certain point you might find important/crucial to explore/learn other tools