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 ?
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Gentle Yang •
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.
Thanks for your focus on this topic. Your word is one of important reasons !
Also there is Strand Life Sciences who make NGS software and also Agilent's GeneSpring GX.
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
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User 7278 •
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.
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User 7278 •
Eagle Genomics in the UK doing NGS and bespoke software.
Its also worth checking the linkedin groups in bioinformatics.
Unipro UGENE, Unipro - a software company from Russia, Novosibirsk, UGENE - it's opensource bioinformatics toolkit
Enlis (just won the Illumina Idea competition). Golden Helix (a lot of people think we at OpenHelix are them...we aren't...)
Integromics has great software for NGS data analysis: SeqSolve
Also, here is a nice list of commercial software for RNA-seq data analysis.
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.
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
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User 1566 •
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.
You could also have a look here : http://www.completegenomics.com/, a compagny offering NGS services based on their own sequencing methodology.
Another big one: DNAnexus
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.
Illumina BaseSpace
This analysis platform integrates Illumina's own tools with others developed by various partners relevant to this question including:
A new one for preprocessing and analyzing systems biology data is InSyBio Ltd. Check it out: http://www.insybio.com/
Try this list: http://grouthbio.com/Genome_Software_Service.php
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.
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Just companies selling software/databases or services as well.
Just companies selling software/databases or services as well?
Yeah,include them .
So many software list but less company/studio list >=<
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.
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