Tutorials

Hands-on walkthroughs of common JBrowse workflows, from first setup to advanced analysis. The first section runs on genomes.jbrowse.org, which hosts a configured JBrowse for every UCSC genome, so those pages need nothing installed and no data prepared.

genomes.jbrowse.org

Basic usage of genomes.jbrowse.org No setup ▶ Video Open a hosted genome, search a gene, and work through the UCSC track catalog on hg38, from conservation at TP53 to filtering a variant catalog down to something readable Synteny on genomes.jbrowse.org No setup ▶ Video Open a UCSC liftOver track in a linear genome view and launch a synteny view from it Proteins on genomes.jbrowse.org No setup ▶ Video Take any gene to its AlphaFold structure and its cross-species protein MSA, launched from the genome view and linked back to it RepeatMasker as one lane per class No setup ▶ Video Split a hub's RepeatMasker track into a labelled lane per repeat class, without preparing any data The HPRC pangenome on genomes.jbrowse.org No setup Draw any window of the HPRC release 2 graph, or a whole chromosome of it, from a hosted page with nothing prepared beforehand

Getting started

JBrowse web quick start Download Set up a self-hosted JBrowse Web instance and add an assembly and tracks JBrowse desktop quick start Download Install JBrowse Desktop, open a genome, and add your first tracks

Synteny & comparative genomics

Synteny visualization (pairwise minimap2) Pipeline ▶ Video Align two assemblies with minimap2 and compare them in the dotplot and linear synteny views Synteny visualization (all-vs-all minimap2) Pipeline ▶ Video Stack strains in a linear synteny view from one all-vs-all PAF Comparing one genome's two haplotypes (T2T-HG002) No setup ▶ Video Load T2T-HG002 v1.2 and the Q100 project's own maternal-to-paternal chain, plot one haplotype against the other genome-wide, and look at the 8p23.1 inversion in a linear synteny view Pangenome (pggb) Pipeline ▶ Video Build a five-strain pggb pangenome graph and load its linear projections plus the graph itself in JBrowse Pangenome (Minigraph-Cactus) Pipeline ▶ Video Build a Minigraph-Cactus pangenome graph and load its linear projections in JBrowse Pangenome (HPRC) No setup ▶ Video Open HPRC release 2's Minigraph-Cactus graph as a graph in the browser, its 464-haplotype variant callset, and the multiple alignment both come from Selection pressure between two genomes (dN/dS) Pipeline Colour an ortholog track by the ratio of non-synonymous to synonymous substitution, and read selection pressure off a gene neighbourhood Synteny from an ortholog table (grape, peach, cacao) Pipeline ▶ Video Stack N genomes from a jcvi MCScan .blocks file Synteny from MCScan anchors (grape, peach) Pipeline ▶ Video Load a pairwise jcvi MCScan run as gene-level and block-level synteny tracks, and convert an MCScanX run into the same files Synteny visualization (a polyploid against itself) Pipeline Draw hexaploid oat against itself from syntenic anchors, coloured by the selection pressure between each pair of copies Synteny visualization (OrthoFinder orthogroups) Pipeline Stack genomes too diverged to align, using OrthoFinder orthogroups as the synteny table

Structural variation

Structural variants (1000 Genomes) No setup ▶ Video Read one whole-gene deletion across the 1000 Genomes cohort, then check the genotypes against the reads that produced them CNV across a population (1000 Genomes) Download Read k-mer depth copy number for every individual in the 1000 Genomes panel, and pack the whole panel into one Zarr store Low-mappability regions (SMN) No setup Check whether a locus can support the calls made on it, using the mappability, coverage and problematic-region tracks genomes.jbrowse.org already publishes Structural variants (Dog10K) Pipeline Genotype four classes of structural variant across dog breeds and read each against the gene it sits in Structural variants from Hi-C No setup ▶ Video Read contact domains and loops off an ENCODE Hi-C matrix, then find a translocation by opening two chromosomes in one view

Cancer genomics

Structural variants (Cancer GIAB) Pipeline ▶ Video Build a tumor/normal HiFi site from raw reads, and read its benchmark SV and CNV calls against the alignments that support them CNV cohort (TCGA) Download ▶ Video Plot somatic copy number across a thousand tumors, one row per sample Complex rearrangements and derivative alleles Pipeline ▶ Video Search a somatic SV callset for rearrangements that take several junctions to make, reconstruct the derivative allele, and check it against the reads Gene fusion calls and the DNA behind them Pipeline Triage a fusion caller's output against the long RNA reads it was called from, then find the DNA break the transcript junction does not sit on Mutation cohort (TCGA) Download ▶ Video Read somatic point mutations across a thousand tumors as a genotype matrix, grouped by clinical annotation Reviewing a whole SV callset ▶ Video Render every junction in a somatic SV callset as a breakpoint image, triage the directory, and check the calls against the matched normal

Population genomics

Selection scans (Drosophila DGRP) Pipeline Fst, diversity, and Tajima's D scans plus per-sample inversion genotypes from one VCF Phased trio analysis (1000 Genomes) Pipeline ▶ Video Paint a child's inherited haplotype blocks from hap-ibd IBD segments, one row per parental copy, and read the crossovers off the track LD at a selective sweep (human) No setup Compute an LD triangle live from phased genotypes, and cut a window that shows the block's edges LD across an inversion (mosquitoes) No setup Read precomputed PLINK LD over a 22 Mb inversion, and load the same inversion genotyped per mosquito QTL mapping (BXD mice) Download ▶ Video Chromosome-painting and a QTL Manhattan plot from GeneNetwork BXD data A loss-of-function allele across breeds (Dog10K) Pipeline Locate a nonsense variant from the reference sequence, then read its genotypes across dog breeds and wolves A selected haplotype (Dog10K) Pipeline ▶ Video Scan the Dog10K panel for allele-frequency differences between breeds at both ends of a trait, then slice one peak out of the SNV callset and cluster its genotype matrix Local ancestry (Dog10K) Pipeline Paint wolf-derived haplotype blocks in two wolfdog breeds, against 219 other breeds and eight held-out wolves, from the Dog10K phased panel

Epigenomics & single cell

Methylation (long-read) No setup ▶ Video Per-read, aggregate, and allele-specific 5mC from HG002 nanopore reads Methylation (bisulfite) Pipeline ▶ Video A WGBS/EM-seq pipeline from SRA reads to per-read CpG/CHG/CHH methylation coloring ChromHMM chromatin states Download ▶ Video Paint many-cell-type ChromHMM states in one multi-row track Single-cell ATAC pseudobulk Pipeline Aggregate single-cell ATAC into per-cell-type coverage BigWigs AlphaGenome predictions No setup Predict expression, accessibility, splicing and 3D contacts over a locus, then score a variant against the reference Single-cell RNA pseudobulk Pipeline Aggregate single-cell RNA into per-cell-type coverage BigWigs, and link them to a UMAP

Transcriptomics & proteins

RNA-seq visualization No setup Spliced reads, splice arcs, and strand-specific coverage in RNA-seq Differential transcript usage Pipeline Build a GFF3 carrying a per-transcript statistic in its attribute column, and configure a gene track to paint it

Configuration & embedding

Cookbook Copy-paste recipes for the most common JBrowse 2 configuration tasks: colors, labels, tooltips, tracks, themes, and more Display settings ▶ Video Change a track's height, color and soft clipping, then make the change stick in a link, a session file, or config.json Embedding JBrowse Embed the linear genome view component in a custom web page JBrowse 2 Embedded component examples ↗ Live, copy-paste examples for the embeddable React components: themes, per-feature colors, sessions, text search, and more. $ jbrowse JBrowse CLI with Desktop Assemble a config.json with the jbrowse CLI and open it in JBrowse Desktop