JBrowse: Visualizing Data Quickly & Easily

Watch the September 24, 2020 BADAS here.


During the 2020 Summer of COVID-19, the Ghedin and Gresham labs sequenced SARS-CoV-2 isolates. To visualize and share this data with collaborators the web-based genome visualization software JBrowse was used https://covid-19.bio.nyu.edu.
To benefit all researchers at NYU engaged in genomics research, a centralized JBrowse service has been published at http://jbrowse.bio.nyu.edu/ for PIs and their lab members.


We’ll go through a demo of 
  • Uploading a dataset
  • How to manipulate the dataset visualization
  • Some features
  • Sharing URLs
Login to the HPC Prince cluster where there is small sample dataset to upload and manipulate. This dataset is located in /beegfs/eb167/yeast. You can see the standard files you are familiar with. There is one file specific to JBrowse and that is the samplelist text file. It is used to tell JBrowse how to group the files after upload, saving you the hassle of manually manipulating the configuration file. To upload, run the following but only change the part in bold and replace with your netID.
cgsb_upload2jbrowse -p demo -d netID -f /beegfs/eb167/yeast
You will be prompted for your password twice in this process, but once you request access to a PI lab passwordless authentication will be configured for you. Let me explain what this command does and the options available.
USAGE: cgsb_upload2jbrowse -p PI -d DATASET [-f FOLDER] [-s SAMPLELIST] [FILES] 
-p | --PI                specify PI 
-d | --dataset           specify data set 
-f | --folder            specify folder containing files 
-s | --samplelist        specify sample list for categorization 
File formats supported: 
- fa 
- fasta 
- fna 
- vcf.gz* 
- bam* 
- bam.bw 
- cram*  
- gff3.gz* 
 *Requires index file (tbi, bai, crai) of the same base name 
Execution of this script will rsync or upload the specified files or folders to the appropriate JBrowse folder, create basic configurations for your dataset, and publish the site. The required fields are -p/–PI for the PI you are a member of and -d/–dataset is for the dataset name that will be visible on the public site. Optional arguments are -f/–folder to recursively upload a folder and its contents as we just did and -s/–samplelist if the file is not named ‘samplelist’. You’ll notice after running the command and if successfully completing you’ll be given a URL link. Something like: https://jbrowse.bio.nyu.edu/demo/?data=data/netID

Other Uploading Options:

Example 2 –

To transfer your data within your scratch (/scratch/user/project1/data) along with the reference data in the prince shared genome repository folders to Smith’s project1 data set run the following.
cgsb_upload2jbrowse -p Smith -d project1 \
 -f /scratch/user/project1/data  \   /scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa \    /scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.34.gff3

Example 3 –

To transfer from outside the Prince cluster
# Transfer the files
rsync --progress -ruv /path/to/dataset/ \ 
# Build and publish the tracks based on the files uploaded
ssh <NYUnetID>@jbrowse.bio.nyu.edu addTracks --PI <PI> --dataset <DATASET>
The data will be accessible immediately on the JBrowse server. Choose your PI on the JBrowse homepage’s dropdown menu then the data set name that was specified in the previous step. Once accessed you will be able to display visualizations or tracks for each file. These tracks by default will be named after the file itself.
Let’s go to the URL of our uploaded yeast dataset. 
On the left we see two blocks labeled combined_ntr_21 and combined_ntr_22. This again was possible because we had a samplelist file listing the prefix used for grouping. If one is not provided it will look like this https://jbrowse.bio.nyu.edu/demo/?data=data/badas-noList.
The available tracks will be selectable on the left allowing you to display only items of interest and their order displayed. 
If you go to the Track menu at the top of the page, you have two options to create a combination track combining 2 tracks or a sequence search track, which shows regions of the referenced sequence or its translations that match a DNA or amino acid sequence.
We can search for features of interest with the search bar at the top.
To the right of the search box we have the highlight button. We can highlight areas of note as well. This is beneficial as the URL will dynamically change based on the current view which includes the highlights. 
You can then use this unique URL to share with colleagues or post in publications. Again this site is open to the public without need for VPN.

Customizing Tracks

We have configured the site to ingest your data in the JBrowse default fashion. You can edit the tracks configuration file (tracks.conf) to meet your needs. For more information on what is possible visit https://jbrowse.org/docs/installation.html

Next Steps

Requesting Permissions

For access, request access through the biology department forms portal at https://forms.bio.nyu.edu. This is separate from HPC access and will require approval from the PI. 
The primary reason being you will have ability to alter or delete all datasets associated with the PI.  The data is not backed up. The only thing that is backed up nightly are the configuration files.

GATK Pipeline

We have integrated automated JBrowse visualization into the GATK pipeline, which performs alignment and variant calling. Within your nextflow.config file add the following lines to specify the data set name and the PI.
// JBrowse params
params.do_jbrowse = true
params.gff = "/scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.34.gff3"
params.jbrowse_pi = "Smith"
params.dataset_name = "project1"

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