jbrowse-plugin-refget-api v1.0.1
jbrowse-plugin-refget-api
This plugin extends a BaseSequenceAdapter to retrieves sequence data from the refget compliant servers
To use this plugin use RefGetAdapter
as the adapter type of the assembly names
RefGetAdapter configuration
The RefGetAdapter contains the following configuration options:
serverLocation (optional)
URL of the refget server, the default value is: https://www.ebi.ac.uk/ena/cram/sequence can be changed to any server compliant with the refget schema
sequenceData (mandatory)
A JSON-like object with the following format:
```
sequenceData: {
sequenceId: {size:number, name:string},
...
}
```
sequenceIdType (optional)
By default is an empty string which means that the sequenceId is an md5 checksum
Example query:
https://www.ebi.ac.uk/ena/cram/sequence/<md5checksum>?start=NNN&end=NNN
Can be changed to insdc
if sequenceId
is the INSDC accession or any other value supported by the refget server.
If not empty the query will be modified as the following:
https://www.ebi.ac.uk/ena/cram/sequence/<sequenceIdType>:<md5checksum>?start=NNN&end=NNN
Configuration
a configuration will look like this:
"assemblies": [
{
"name": "assemblyName",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "refseq_track",
"adapter": {
"type": "RefGetAdapter",
"serverLocation": { // optional
"uri": "https://www.ebi.ac.uk/ena/cram/sequence" //url of the server + /secuence endpoint
},
"sequenceIdType": "", // optional
"sequenceData": { // mandatory
"md5checksum1": {name: chr1, size: 1000000},
"md5checksum2": {name: chr2, size: 920300},
}
}
}
}
]
To use in @jbrowse/react-linear-genome-view
install it via npm
To use in jbrowse-web
Add to the "plugins" of your JBrowse Web config:
{
"plugins": [
{
"name": "RefGet",
"url": "https://unpkg.com/jbrowse-plugin-refget-api/dist/jbrowse-plugin-refget-api.umd.production.min.js"
}
]
}
You can also download this file to your local server if you don't want to use a CDN