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JBrowse Genome Browser

JBrowse is a web-based genome browser for visualizing genomic features in common file formats, such as variants (VCF), genes (GFF3, BigBed) and gene expression (BigWig), and sequence alignments (BAM, CRAM, and GFF3).

Getting started​

$ cd /path/to/data_directory
$ ls 
alignments.sorted.bam
alignments.sorted.bam.bai
expression.bw
genes.gff3     
genes.gff3.tbi  
reference.fa.       
reference.fa.fai    
tracks.conf
variants.sorted.vcf.gz 
variants.sorted.vcf.gz.tbi

Commonly used genomic data sets are available from the Shared Genome Resource. The data is stored in a common location with the following naming convention:

/scratch/work/cgsb/genomes/Public/<KINGDOM>/<SPECIES>/<SOURCE>/<VERSION>/
tip

There is no need to copy the reference or GFF3 to your data directory. This would just waste space. You should link the files you'd like to your data directory as shown below:

$ ln -s /scratch/work/cgsb/genomes/.../reference.fa reference.fa
$ ln -s /scratch/work/cgsb/genomes/.../reference.fai reference.fai
$ ln -s /scratch/work/cgsb/genomes/.../genes.gff3 genes.gff3
$ ln -s /scratch/work/cgsb/genomes/.../genes.gff3.tbi genes.gff3.tbi

2. Verify data files are in a supported format​

For the commands listed below, bgzip and tabix are provided by the htslib module. samtools and bcftools are provided by the module of the same name. (use module avail htslib samtools bcftools to list the installed versions)

FA​

If the reference and index are not available in the Shared Genome Resource, it should be compressed with bgzip and indexed with samtools faidx.

bgzip reference.fa
samtools faidx reference.fa.gz

GFF3​

If the GFF3 is not available in the Shared Genome Resource, the file should first be sorted by seqid (column 1) and start (column 4), compressed with bgzip, and indexed with tabix.

awk -F '\t' 'NF == 9' genes.gff3 | sort -k 1,1 -k 4n,4n | bgzip > genes.sorted.gff3.gz
tabix -p gff genes.sorted.gff3.gz

The above command generates a GFF3 lacking directives/comments found in the original, but they not necessary for viewing in JBrowse.

BED​

A number of BED file formats can be displayed after sorting by chrom (column 1) then chromStart (column 2), compressed with bgzip, and indexed with tabix.

sort -k 1,1 -k 2n,2n peaks.bed | bgzip > peaks.sorted.bed.gz
tabix -p bed peaks.sorted.bed.gz

BAM/CRAM​

BAM and CRAM files must be sorted with samtools sort and indexed with samtools index.

samtools sort -o alignments.sorted.bam my.bam
samtools index alignments.sorted.bam

For large BAM files, use the --threads option to set the number of threads for sorting, the -m option to specify the amount of memory per thread, and the -l option to set compression level for the resulting BAM file.

VCF​

VCF files should be sorted with bcftools and indexed with tabix.

bcftools sort --output-type=z --output-file=variants.sorted.vcf.gz variants.vcf
tabix -p vcf variants.sorted.vcf.gz

For large VCF files (above ~768M), the bcftools --max-mem option may be used to allocate extra memory for sorting VCF records, avoiding the use of the file system for an external merge sort.

3. Create the configuration file, tracks.conf​

An example of a minimal configuration

[GENERAL]
refSeqs=reference.fa.gz.fai
# reference sequence compressed with bgzip & indexed with "samtools faidx"
## If using Shared Genome Resource where file is uncompressed
## refSeqs=reference.fa.fai

[tracks.reference]
urlTemplate=reference.fa.gz
# file specified as the refSeqs value without the ".fai" suffix
## If using Shared Genome Resource where file is uncompressed
## urlTemplate=reference.fa.

[tracks.alignments]
urlTemplate=alignments.sorted.bam
# my.sorted.bam.bai (created by "samtools index") is assumed to exist
## baiUrlTemplate=alignments.sorted.bai
# custom name if corresponding .bai file isn't suffixed with .bam.bai

[tracks.variants]
urlTemplate=variants.sorted.vcf.gz
# variants.sorted.vcf.gz.tbi assumed to exist

[tracks.genes]
urlTemplate=genes.sorted.gff3.gz
# genes.sorted.gff3.gz.tbi assumed to exist
## If using Shared Genome Resource where file is uncompressed
## you must create the tbi index with tabix.
## urlTemplate=genes.sorted.gff3

[tracks.expression]
urlTemplate=expression.bw

[tracks.peaks]
urlTemplate=peaks.bed.gz
# peaks.bed.gz.tbi assumed to exist

Customizing Tracks:

4. Making feature names searchable in JBrowse (Optional)​

The JBrowse generate-names.pl script generates an index of feature names for searching and autocompletion when typed into the JBrowse search box, or the View > search for features menu option.

module load jbrowse/web/1.16.0
generate-names.pl --compress --out .

Configuration​

Enter the full path to the directory you created above in the Data Folder Path input, add any optional Slurm options and press the Launch button.

JBrowse running in OOD​

After a short pause while your job is in the Greene queue and then starts up, you'll see the JBrowse application.