Question: Software For Analysis Of Bacterial Genomics.
3
gravatar for Nari
4.6 years ago by
Nari810
United States
Nari810 wrote:

Hi, everyone, I work on microbial genomes.Do anyone know an all in one software which can be useful for me to study all aspects of bacterial genome data?
A single software which is able to perform various tasks like multiple genome alignments, phylogenetic studies , genome visualizations, SNP analysis, *core and dispensable genome visualizations and many such things* will be highly acceptable.
I can manage funds upto 2500 USD.
Thanks in advance.

genome analysis • 4.9k views
ADD COMMENTlink modified 4.6 years ago by Jeroen Van Goey2.1k • written 4.6 years ago by Nari810
2

This very much depends on your bioinformatic skills - and backing.

ADD REPLYlink written 4.6 years ago by Martin A Hansen3.0k
1

Galaxy ( https://main.g2.bx.psu.edu/ ) ? But it's free...

ADD REPLYlink written 4.6 years ago by Manu Prestat3.8k
5
gravatar for Josh Herr
4.6 years ago by
Josh Herr5.4k
University of Nebraska
Josh Herr5.4k wrote:

I think finding one program to do it all is the easy way out: You'll understand more and have more control if you use specific tools designed for each respective job.

That being said, if I was to recommend a single program I think the CLC bio platform (genomics workbench or main workbench) is quite good. The genome alignment and visualization aspects might be a bit lacking for you compared to other resources, but it's basically a complete package. There are plugins to add to its functionality.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Josh Herr5.4k

Thanks. sorry I forgot to add "bacterial core and dispensable genome visualization plots" in my question.

ADD REPLYlink modified 4.6 years ago by Josh Herr5.4k • written 4.6 years ago by Nari810

That's okay. I'm not sure what "core and dispensable genome visualizations and many such things" means anyway.

ADD REPLYlink written 4.6 years ago by Josh Herr5.4k
2
gravatar for ALchEmiXt
4.6 years ago by
ALchEmiXt1.8k
The Netherlands
ALchEmiXt1.8k wrote:

You might be interested in a comparable package called Lasergene from DNAstar.

However I agree with Josh that individual tools might be better to tune what you actually want.

Have you checked out the free NCBI Genomics Workbench and Ugene already? They can do most as well.

enter image description here

ADD COMMENTlink written 4.6 years ago by ALchEmiXt1.8k

Both freewares are quite useful but sorry I forgot to add "bacterial core and dispensable genome visualization plots" in my question. what I require too.

ADD REPLYlink written 4.6 years ago by Nari810

Can you supply more info on what you mean by "bacterial core and dispensable genome visualization plots"?. You mean something like horizontal genetransfer modules or so-called Locally Collinear Blocks?

ADD REPLYlink written 4.6 years ago by ALchEmiXt1.8k

what I meant by 'core and dispensable genome visualizations' is that, Creating Ortholog clusters from many genomes same as CD-HIT server also plot fall in number of core genes and rise in dispensable genes as each new genome is added to the dataset. Same as this image for example: http://genomebiology.com/2007/8/5/R71/figure/F2

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Nari810
2
gravatar for Jeroen Van Goey
4.6 years ago by
Jeroen Van Goey2.1k
Ghent, Belgium
Jeroen Van Goey2.1k wrote:

BioNumerics is the all-in -one solution you are looking for (disclaimer: I work for Applied Maths, the company that develops BioNumerics). It is extensively used for studying all aspects of bacterial genome data. Specifically, for the areas you are interested in:

  • multiple genome alignments: "The Genome Analysis Tools module offers side-by-side comparison of genomes and chromosomes, analysis of organization and functional behavior of genomes, alignment of multiple chromosomes and chromosome-based SNP analysis." multiple genome alignments

  • phylogenetic studies: "BioNumerics offers Maximum Parsimony and Maximum Likelihood as phylogenetic inference methods. Besides standard algorithms, the optimal trees can be calculated using simulated annealing or quartet puzzling. Both methods result in an unrooted tree, which can be converted into a rooted tree after assignment of a root. To correct phylogenetic distance scaling, the Jukes & Cantor or Kimura 2 parameter correction factors can be chosen."

    Dendrogram features

  • SNP analysis: "BioNumerics’ sequence alignment application is an invaluable tool for SNP and mutation analysis. SNPs or mutations are screened for through up to many thousands of aligned sequences. The software statistically calculates the probability of each SNP based upon the quality of the base assignments and the curves in the chromatogram files. Various filters allow for screening SNPs with specific thresholds or other features such as the type of mutation they induce. By looking at sequencer chromatograms directly, the user has excellent control over the probability of each potential SNP locus. Complete alignments, including all SNP and subsequence search listings, can be saved and re-edited at any time. Additional sequences can be added to existing projects." SNP analysis

I am not completely sure what you mean by 'core and dispensable genome visualizations', but if there is something you really need/want that currently is not available in the software, then we can always write a custom script for you to add that functionality.

Please contact our sales department for a free evaluation software license or to request a quote.

ADD COMMENTlink modified 19 months ago • written 4.6 years ago by Jeroen Van Goey2.1k
4

That looks pretty nifty! The truth is that when it comes to visualization there are a lot fewer open source options - and the commercial solutions always seem better.

I think it has to do with the fact that open source thrives when the quality metrics are "objective": Faster, more accurate, fewer resources.

When it comes to what looks good or makes sense the metrics are subjective and it is not immediately obvious which option is better - hence the open source meritocracy does not work that well.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Istvan Albert ♦♦ 73k

@Jeroen: Of course I need all above functionality, (in addition) what I meant by 'core and dispensable genome visualizations' is that, Creating Ortholog clusters from many genomes same as CD-HIT server also plot fall in number of core genes and rise in dispensable genes as each new genome is added to the dataset. Same as this image for example: http://genomebiology.com/2007/8/5/R71/figure/F2

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Nari810
1

@/Vari: I have sent you an e-mail with some more information.

ADD REPLYlink written 4.6 years ago by Jeroen Van Goey2.1k
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