Question: Is There A List Of Top N Bioinformatics Or Genome Software Company Or Studio ?
12
gravatar for Gentle Yang
7.0 years ago by
Gentle Yang190
Shenzhen,China
Gentle Yang190 wrote:

I know NCBI, EBI, Ensembl or more other bioinformation database ,and MAQ, SOAP, BWA ... more other softwares. But most are from big genome center or sequence group. So I wanna know if there is some pure software company or studio who develop software in Bioinformatics and Genomics ,and who are they ?

genome software • 16k views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 7.0 years ago by Gentle Yang190

Just companies selling software/databases or services as well?

ADD REPLYlink written 6.9 years ago by Mndoci1.2k

Yeah,include them .

ADD REPLYlink written 6.9 years ago by Gentle Yang190

So many software list but less company/studio list >=<

ADD REPLYlink written 6.7 years ago by Gentle Yang190

Our company, Creative Bioinformatics Consultants www.creativebioinformatics.com) provides user-directed, customized data analysis and software creation for small-to-medium sized projects from academic labs and biotechnology companies that do not have the capabilities or resources to do the work in house. Please contact us via our website or at creativebioinformatics@gmail.com to discuss your project and receive a quote.

ADD REPLYlink written 4.4 years ago by creativebioinformatics0

Avadis NGS from Strand Lifesciences, is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, and ChIP-Seq experiments.

Avadis NGS comes pre-packaged with comprehensive annotations for several standard organisms from various sources and enables you to create annotations for other organisms. It includes an embedded feature-rich Genome Browser and provides custom visualizations to provide an intuitive feel for analysis results. Various quality control plots and filtering steps ensure that any poor quality data is kept out of downstream analysis. Biological interpretation and discovery tools such as Gene Ontology enrichment, GSEA, NLP derived interaction network analysis, and significant pathways analysis enable taking the analysis all the way from reads to the end goal of the experiment. For more information visit www.avadis-ngs.com

ADD REPLYlink written 4.1 years ago by yeshodari0
7
gravatar for Neilfws
7.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

There are some companies of that kind. I'll start: CLC bio.

The problem for companies that specialize in bioinformatics software is that they have to sell it, in the face of (1) a small market and (2) a huge number of free, open-source solutions. So they have to be very good.

ADD COMMENTlink written 7.0 years ago by Neilfws48k

Thanks for your focus on this topic. Your word is one of important reasons !

ADD REPLYlink written 7.0 years ago by Gentle Yang190
6
gravatar for Pasta
7.0 years ago by
Pasta1.3k
Switzerland
Pasta1.3k wrote:

And of course: Partek with its excellent Genomic Suite

ADD COMMENTlink written 7.0 years ago by Pasta1.3k
3
gravatar for lh3
7.0 years ago by
lh330k
United States
lh330k wrote:

NovoCraft. I am quite impressed by novoalign. BTW, they quote my words on their homepage. By "to date", I mean the end of 2009. I have not systematically evaluated which aligner is the most accurate nowadays.

ADD COMMENTlink written 7.0 years ago by lh330k
2
gravatar for Daniel Swan
7.0 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

Also there is Strand Life Sciences who make NGS software and also Agilent's GeneSpring GX.

ADD COMMENTlink written 7.0 years ago by Daniel Swan13k

Strand's NGS software is called Avadis NGS and it is built on the same technology platform as GeneSpring (which Strand develops for Agilent). Avadis NGS is well documented on its website: http://avadis-ngs.com

ADD REPLYlink written 6.8 years ago by User 727820

Strand's NGS software is called Avadis NGS and it is built on the same technology platform as GeneSpring (which Strand develops for Agilent). Avadis NGS is well documented on its website: http://avadis-ngs.com. Try it out if you are working with post-alignment RNA, DNA, or ChIP-Seq data.

ADD REPLYlink written 6.8 years ago by User 727820
2
gravatar for Niallhaslam
7.0 years ago by
Niallhaslam2.2k
Dublin
Niallhaslam2.2k wrote:

Eagle Genomics in the UK doing NGS and bespoke software.

Its also worth checking the linkedin groups in bioinformatics.

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Niallhaslam2.2k
2
gravatar for Casey Bergman
7.0 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

A couple others:

ADD COMMENTlink written 7.0 years ago by Casey Bergman17k
1
gravatar for Mary
7.0 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Enlis (just won the Illumina Idea competition). Golden Helix (a lot of people think we at OpenHelix are them...we aren't...)

ADD COMMENTlink written 7.0 years ago by Mary11k
1
gravatar for Hranjeev
7.0 years ago by
Hranjeev1.4k
Malaysia
Hranjeev1.4k wrote:

Synamatix a bioinformatics company operating from South East Asia.

ADD COMMENTlink written 7.0 years ago by Hranjeev1.4k
1
gravatar for Anonymous
7.0 years ago by
Anonymous10
Anonymous10 wrote:

Integromics has great software for NGS data analysis: SeqSolve

Also, here is a nice list of commercial software for RNA-seq data analysis.

ADD COMMENTlink written 7.0 years ago by Anonymous10
1
gravatar for Len Trigg
7.0 years ago by
Len Trigg1.1k
New Zealand
Len Trigg1.1k wrote:

Real Time Genomics produces the RTG Investigator suite for NGS mapping and variant detection. AFAIK RTG is the only mapping tool that supports Complete Genomics read data.

ADD COMMENTlink written 7.0 years ago by Len Trigg1.1k
1
gravatar for User 1566
6.9 years ago by
User 156610
User 156610 wrote:

There is a List of Next Generation Sequence Analysis/Tools at http://www.g6g-softwaredirectory.com/ and the corresponding companies that make this software are also listed...

Al Shapiro

ADD COMMENTlink written 6.9 years ago by User 156610
1
gravatar for vaskin90
4.5 years ago by
vaskin90260
Milan, Italy
vaskin90260 wrote:

Unipro UGENE, Unipro - a software company from Russia, Novosibirsk, UGENE - it's opensource bioinformatics toolkit

ADD COMMENTlink written 4.5 years ago by vaskin90260
0
gravatar for User 7278
6.8 years ago by
User 727820
User 727820 wrote:

Check out Avadis NGS if you have to analyze RNA-Seq, ChIP-Seq, whole genome, or exome sequence data.

It is a commercial package, but features like genome browser visualizations, statistics, and packages for annotations and pathways (including Biobase) are handy for people who have limited experience with open source programs.

The same bioinformatics team is behind GeneSpring, great for those accustomed to that UI.

ADD COMMENTlink written 6.8 years ago by User 727820
0
gravatar for toni
6.8 years ago by
toni2.1k
Lyon
toni2.1k wrote:

You could also have a look here : http://www.completegenomics.com/, a compagny offering NGS services based on their own sequencing methodology.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by toni2.1k
0
gravatar for Manu Prestat
5.1 years ago by
Manu Prestat3.8k
Marseille, France
Manu Prestat3.8k wrote:

Another big one: DNAnexus

ADD COMMENTlink written 5.1 years ago by Manu Prestat3.8k
0
gravatar for geoffhrouth
4.9 years ago by
geoffhrouth0 wrote:

I started one about a year ago at www.grouthbio.com. I'm trying to be inclusive, so it may not be a list of just the top selling ones. But you may find it interesting.

ADD COMMENTlink written 4.9 years ago by geoffhrouth0
0
gravatar for Malachi Griffith
4.9 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith16k wrote:

Illumina BaseSpace

This analysis platform integrates Illumina's own tools with others developed by various partners relevant to this question including:

  • Strand (Elastic Genome Browser)
  • Golden Helix (Genome Browse)
  • Broad Institute of MIT and Harvard (IGV)
  • Biomatters (The Molecular Profiler)
  • SciGenom (OncoMD)
  • Omicia (Opal Launcher)
  • Partek (Partek Flow)
  • DNASTAR (SeqMan NGen)
  • Syapse (Syapse Discovery)
  • Elsevier (Genomics Data)
  • Omixon Biocomputing (HLA Typing)
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Malachi Griffith16k
0
gravatar for theofilk
4.5 years ago by
theofilk0
theofilk0 wrote:

A new one for preprocessing and analyzing systems biology data is InSyBio Ltd. Check it out: http://www.insybio.com/

ADD COMMENTlink written 4.5 years ago by theofilk0
0
gravatar for David Langenberger
4.5 years ago by
Deutschland
David Langenberger8.1k wrote:

Try this list: http://grouthbio.com/Genome_Software_Service.php

ADD COMMENTlink written 4.5 years ago by David Langenberger8.1k
0
gravatar for creativebioinformatics
4.4 years ago by

Our company, Creative Bioinformatics Consultants www.creativebioinformatics.com) provides user-directed, customized data analysis and software creation for small-to-medium sized projects from academic labs and biotechnology companies that do not have the capabilities or resources to do the work in house. Please contact us via our website or at creativebioinformatics@gmail.com to discuss your project and receive a quote.

ADD COMMENTlink written 4.4 years ago by creativebioinformatics0
0
gravatar for kalina
2.3 years ago by
kalina0
kalina0 wrote:

You could also take a look at GenestackĀ 

ADD COMMENTlink written 2.3 years ago by kalina0
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