| | 1 | = Genome browser review = |
| | 2 | |
| | 3 | An overview of genome browsers can be found at http://en.wikipedia.org/wiki/Genome_browser and tried them. Things that make them unsuitable (for integration) in my opinion are: |
| | 4 | |
| | 5 | * Very limited application: e.g. aimed at just viral genomes or ChIP-seq data |
| | 6 | * Externally hosted webapp, but not able to accept any custom user tracks |
| | 7 | * Standalone application (e.g. download a JAR) which is very hard or impossible to integrate |
| | 8 | * Not prefilled with community data, no added value (after starting, you get an empty screen, and you should import everything yourself) |
| | 9 | |
| | 10 | So that took care of most of them. Left are: |
| | 11 | * UCSC / Ensembl / NCBI style (an externally hosted webapp) |
| | 12 | * jBrowse/GBrowse style (a self hosted webapp - typically, let's assume this for now) |
| | 13 | |
| | 14 | Pro's/Con's for UCSC (et al):[[BR]] |
| | 15 | * (+) Hosted, updated and maintained for you, saved a lot of trouble[[BR]] |
| | 16 | * (+) Many existing tracks, and more added gradually[[BR]] |
| | 17 | * (+) Ability to add custom tracks[[BR]] |
| | 18 | * (+) Accepts many formats[[BR]] |
| | 19 | * (-) Must upload to an external service, so performance is probably bad (though optimizable with very specific formats/services)[[BR]] |
| | 20 | * (-) Makes your app dependent on an external service |
| | 21 | |
| | 22 | Pro's/Con's for jBrowse (et al):[[BR]] |
| | 23 | * (+) Host by yourself, so completely customizable, update whenever you want, uptime is under your control[[BR]] |
| | 24 | * (+) Ability to add custom tracks[[BR]] |
| | 25 | * (+) Accepts not so many formats, but can also run on top of databases[[BR]] |
| | 26 | * (+) Runs locally on your own files, so good performance[[BR]] |
| | 27 | * (-) Effort to set it up, keep it running, update it, fix problems or security breaches yourself, etc[[BR]] |
| | 28 | * (-) Little or no default tracks, must setup and update the content yourself |
| | 29 | |
| | 30 | Supplements: |
| | 31 | |
| | 32 | * If you want, you can checkout the code + data for the UCSC or Ensembl browser to run a local mirror: |
| | 33 | Better for performance, but these tools are not light-weight systems, so maintenance can quickly become a full-time job... |
| | 34 | (if you want to support all species / data sets) |
| | 35 | * The Ensembl browser is much more advanced: requires a bit more tweaking of the settings to your personal needs, |
| | 36 | but it always surprises me when people prefer to stick to the dated UCSC browser... |
| | 37 | |
