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Config editing quick start — command-line interface

In order to display your data, JBrowse 2 needs to know about the reference genome for your organism of interest and needs to have tracks created that reference your data sources. This guide will show you how to set those up using the JBrowse CLI.

note

You can also do this configuration with graphical configuration editing interface built into JBrowse 2. See that guide here.

Pre-requisites

Adding a genome assembly

info

For this step we configure JBrowse to use files being hosted at a URL. For an example of how to use files located on your computer, see the adding a track step.

First we will configure an assembly, or reference genome, for for JBrowse 2. This usually means providing a file that describes the reference sequence for the organism, such as a FASTA or 2BIT file.

You will want to use your own data for your organism, but for this example we provide a small example reference sequence for a simulated organism, volvox mythicus, that you can use.

# Make sure you are in the directory where you have downloaded JBrowse 2
jbrowse add-assembly http://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.fa
caution

A FASTA must have an index to work in JBrowse 2. This command assumes that the index file is the same as the FASTA but with .fai appended to the file name.

This command will generate a config file if one does not exist yet and add an assembly called "volvox" to the config file with the URLs of the FASTA and FASTA index files. The name of the assembly was guessed from the file name, but you can customize that and many other things with various flags passed to the command. You can run jbrowse add-assembly --help to get a list of all the options.

JBrowse 2 also supports other assembly file formats, such as bgzip-compressed indexed FASTA (e.g. .fa.gz, .fa.gz.fai, and .fa.gz.gzi files) and 2BIT files. See configuring assemblies for more info on formats supported for the sequence file.

note

If your FASTA is not indexed, you can use the samtools tool to index it.

samtools faidx volvox.fa
# generates volvox.fa.fai

Or if you want to compress your FASTA, you can use bgzip as well.

bgzip volvox.fa
samtools faidx volvox.fa.gz
# compresses volvox.fa to volvox.fa.gz and generates volvox.fa.gz.fai and volvox.fa.gz.gzi

For more info about bgzip and samtools, see https://www.htslib.org/.

If you have your JBrowse 2 running as described in the JBrowse web quickstart, you can refresh the page and an add a linear genome view. You will now see your config in the Assembly dropdown.

JBrowse 2 linear genome view setup with volvox in assembly dropdown
Figure: JBrowse 2 linear genome view setup with volvox in assembly dropdown

Adding a track

Now we will show you how to add an alignments track and a variant track to JBrowse 2.

info

For this step we configure JBrowse to use files located on your computer. For an example of how to use files hosted at a URL, see the adding a genome assembly step.

Adding an alignments track

For this example we will use a BAM file to add an alignments track. Again, for this example we provide a small example BAM, but for your data you will replace the file name with the names of your data files.

For this track we will assume the data is on your computer at the locations /data/volvox.bam and /data/volvox.bam.bai. You can download these file here if you want to run this example: BAM and BAM index.

To add the track, run

# Replace with the location of your BAM file
jbrowse add-track /data/volvox.bam --load copy

This will copy the BAM and BAM index into the JBrowse 2 directory and add a track pointing at those files to the config file. To see more options adding the track, such as specifying a name, run jbrowse add-track --help.

If you don't want to copy your BAM file, you can use --move to move the file into the JBrowse 2 directory or --symlink to add a symlink to the file to the JBrowse 2 directory. If you want more control over the location, you can use inPlace to point the track at the file where it is, but be careful with this option because on a traditional server you will need to ensure that the file is in a place where the web server is serving it.

note

If your BAM is not indexed, you can use the samtools tool to index it.

samtools index volvox.bam
# generates volvox.bam.bai

For more info about samtools, see https://www.htslib.org/.

If you have your JBrowse 2 running as described in the JBrowse web quickstart, you can refresh the page and an add a linear genome view of the volvox assembly. Then open track selector, and you will see the alignments track.

JBrowse 2 linear genome view with alignments track
Figure: JBrowse 2 linear genome view with alignments track

Adding a variant track

Adding a variant track is similar to adding an alignments track. For this example, we will use a VCF file for the track. JBrowse 2 expects VCFs to be compressed with bgzip and indexed. Similar to the above example, we will assume the files are at /data/volvox.vcf.gz and /data/volvox.vcf.gz.tbi. You can download these file here: VCF and VCF index.

To add the track, run

jbrowse add-track /data/volvox.vcf.gz --load copy
note

If your VCF is not indexed, you can use the bgzip and tabix tools to compress index it.

bgzip yourfile.vcf
tabix yourfile.vcf.gz

Alternatively, you can do the same thing with the bcftools tool.

bcftools view volvox.vcf --output-type z > volvox.vcf.gz
rm volvox.vcf
bcftools index --tbi volvox.vcf.gz

Note if you get errors about your VCF file not being sorted when using tabix, you can use bcftools to sort your VCF.

bcftools sort file.vcf > file.sorted.vcf
bgzip file.sorted.vcf
tabix file.sorted.vcf.gz

For more info about bgzip, tabix, and bcftools, see https://www.htslib.org/.

If you have your JBrowse 2 running as described in the JBrowse web quickstart, you can refresh the page and an add a linear genome view of the volvox assembly. Then open track selector, and you will see the variant track.

JBrowse 2 linear genome view with variant track
Figure: JBrowse 2 linear genome view with variant track

Adding a BigWig/BigBed track

Probably one of the most simple track types to load is a BigWig/BigBed file since it does not have any external index file, it is just a single file

An example file is here https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox-sorted.bam.coverage.bw

## Download bigwig or bigbed file
jbrowse add-track volvox-sorted.bam.coverage.bw --load copy

Adding a GFF3 file with GFF3Tabix

To load a GFF3 file, we can sort and index it with tabix

Sorting a GFF3 can be done with GenomeTools (to install can use sudo apt install genometools)

gt gff3 -sortlines -tidy -retainids yourfile.gff > yourfile.sorted.gff
bgzip yourfile.sorted.gff
tabix yourfile.sorted.gff.gz
jbrowse add-track yourfile.sorted.gff.gz --load copy

Indexing feature names for searching

The final step of loading you jbrowse instance may include adding a "search index" so that you can search by genes or other features by their name or ID

To do this we can use the jbrowse text-index command

jbrowse text-index

This will index relevant track types e.g. any track with Gff3TabixAdapter (gene names and IDs) or VcfTabixAdapter (e.g. variant IDs). The command will print out a progress bar for each track that it is indexing.

This will also update your config.json so after it completes, you can type a gene name into the "search box" in the linear genome view or other views and quickly navigate to genes by gene name.

See the text-index command docs for more info. Also see the FAQ entries for text searching

Conclusion

Now that you have JBrowse configured with an assembly and a couple of tracks, you can start customizing it further. Check out the rest of the docs for more information, especially the JBrowse CLI docs for more details on some of the steps shown here.