Originally posted by Inti
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Since Inti asked and no one replied, may I jump in here.
I am from Genomatix and may have a rather biased view
With the increasing data load from NGS, we decided to move from web based services to delivering turnkey systems on site.
Currently there are two offerings:
ATTENTION commercial advertizing following:
Genomatix delivers powerful turnkey solutions downstream of Next Generation Sequencing (NGS) devices, following the Genomatix tradition of highest scientific standards and cutting edge technology.
Genomatix solutions work with data from all available NGS system providers: Illumina´s Genome Analyzer (Solexa), Roche (454), The SOLiD TM System by Applied Biosystems, and HeliScope by Helicos.
Genomatix Mapping Station (GMS) delivers ultra-fast mapping of sequence reads of any length above 9 base pairs. Ten million typical NGS reads of variable lengths are perfectly and uniquely mapped to the human genome in less than 30 minutes. GMS is flexible and allows for any number of indels and point mutations, delivering an uniqueness measure for each mapped read. It takes the NGS system internal error checking into account and detects new SNPs. Cutting edge technology identifies splice junction tags for advanced transcriptome analysis.
Genomatix Genome Analyzer (GGA) is the complete solution for ChIP-seq and transcriptome analysis downstream of mapping the NGS system reads to the genome with the Genomatix Mapping Station, or any other technology. Terabytes of annotation data complement the results from the NGS experiment and expand by optional integration with each new sequencing run to a customized genome database. Easy-to-use visualization and genome wide correlations allow for meta-analysis of all kind of data-sets.
Integrated comparative genomics procedures allow for phylogenetical conservation analysis of findings.
Genome wide transcription factor analysis, gene regulatory region analysis, regulatory SNPs, epigenetic modification analysis, DNase-seq, digital gene expression with normalization and quantification of expression values… all required data and hardware in one technology unit at your lab. GGA is operated through a comprehensive easy-to-use web based interface for the biologist, plus features full data structure access and command line driven procedures for the bio-informatician for easy integration into own high-throughput pipelines
End of commercial advertizing
The above would fit to integrated solutions.
The following solutions are web-based and free for everybody up to two weeks after signing up for a test account.
ChIP-Seq. RegionMiner
Genome Annotation/Genome Browser: ElDorado
Personal annotation up to 10 times 10 million regions can be uploaded into ElDorado through RegionMiner.
Then, Genomatix offers analysis services
Example data for Boyle´s Solexa DNase-seq data is here
(lower picture is clickable)
Sorry, if this posting is too commercial. I promise, I won´t do it again
Klaus
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