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 ?
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.
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.
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)
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