jbrowse-plugin-hgb


JBrowse2 plugin for displaying long-read alignments by hgb.

Screenshots


Prerequisites

* Rust nightly (cargo)
* Node.js

Getting Started

The input bam file needs to be attached MD tags by samtools calmd and indexed by samtools index.

* Docker

``bash
docker run --rm -ti -p 9000:9000 -v pwd:/data 6thbridge/jbrowse2-hgb:master /data/
`

* Singularity

`bash
singularity build jb2-hgb.sif docker://6thbridge/jbrowse2-hgb:master
singularity -s run jb2-hgb.sif
`

Access to http://localhost:9000/static/index.html.

Manual Deploy

$3

`bash
bash -x start_hgb_server.sh $NUM_OF_THREADS $LOCATION_OF_BAM
bash -x start_hgb_server.sh $NUM_OF_THREADS $LOCATION_OF_BAM 0.0.0.0:5000
`

$3

The following command needs to run on another shell.

`bash
bash -x start_jbrowse_hgb.sh
bash -x start_jbrowse_hgb.sh $HGB_SERVER_URL 38
bash -x start_jbrowse_hgb.sh $HGB_SERVER_URL 19
`

You can specify reference genome as the second argument as 38 or 19 (hg38 or hg19, respectively).

Usage in jbrowse-web

Add to the "plugins" of your JBrowse Web config. The unpkg CDN should be stable, or you can download the js file to your server

`json
{
"plugins": [
{
"name": "hgb",
"url": "https://unpkg.com/jbrowse-plugin-hgb/dist/jbrowse-plugin-hgb.umd.production.min.js"
}
]
}
``

This plugin is currently quite basic, and there is no mouseover interactivity or drawn labels on features

$3

See DEVELOPMENT