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Personalized Genome Analysis

Page history last edited by Administrator 10 years, 8 months ago

Personal Genome Analysis Wiki

Back to the main Open Thought Space

 

Next-generation tools are starting to proliferate for personalized genomic data analysis. How soon can we launch the first GenomeCamp? Please email me with any additions, modifications, deletions or comments.

 

  1. Crossbow (UMD/College Park, MD): a scalable software pipeline for whole genome resequencing analysis. It combines Bowtie, an ultrafast and memory efficient short read aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and accelerate the computation with many nodes. The pipeline can accurately analyze over 35x coverage of a human genome in one day on a 10-node local cluster, or in 3 hours for about $100 using a 40-node, 320-core cluster rented from Amazon's EC2 utility computing service. News article: Analyzing Human Genomes with Hadoop

  2. DNA Guide (Sebastopol, CA): uses Geographic Information Systems technology to create a personal Map of the genome with all the chromosomes of a person with map layers added for sequence and SNP data. A coordinate system allows pannning and zooming functionality like Google Earth for the cell. At the zoom in level each individual DNA base pair is its own programmable graphic object. News article: DNA Guide presents live demo of personal genome management software using Geographic Information Systems at Health 2.0

  3. DNAnexus (Palo Alto, CA): DNAnexus is a start-up in biocomputation aiming to transform the future of genomic analysis. The rapid advancement of DNA sequencing technologies will one day enable one of the holy grails of medicine: the personal genome. But it is also unleashing a torrent of data that needs to be managed and analyzed. DNAnexus is leveraging modern web technologies on a cloud computing infrastructure to create a compute platform for the genome era. DNAnexus is backed by a collection of leading investors, including early-stage VC First Round Capital ($1.55 m Series A round raised 8/3/09 primarily from First Round Capital) and comprises a team of individuals that include MIT alumni, Stanford PhDs in computational genomics, and Professors in Computer Science, Genetics, and Pathology (Andreas Sundquist, Serafim Batzoglou).

  4. Ewakening (Sunnyvale, CA): Personal genomics community

  5. GenoViz (SourceForge.net): Tools for genomic data visualization, a three-part kit: GenoViz SDK (software development kit) is a library of re-usable components for genomics data visualization. Genometry is a unified data model to represent relationships between biological sequences. It is mainly used in the Integrated Genome Browser (IGB, pronounced "ig-bee") is a desktop application that uses both the GenoViz SDK and Genometry. It supports visualization and exploration of genes, genomes, and genome-scale data sets, especially data from genome tiling arrays. IGB can display data from multiple data sources, including DAS (Distributed Annotation System) servers and local files on your file system.
  6. SNP Dr. from DNA Electronics (London, UK): SNP Dr. hand-held lab-on-a-chip device for point-of-care SNP sequencing in 15-30 minutes to evaluate patient drug response. News article: "DNA Electronics has a hand held Genetic Testing Device - Interview with CEO"
  7. SNPedia (Netherlands): Open-source database where 35 people have publicly shared their genomes. SNPedia provides information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain personal DNA data.
  8. Portable Genomics (France): smartphone genome browser.

 

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