User guide
How to drive JBrowse once it is running. New here? Start with the JBrowse Web or JBrowse Desktop quickstart.
General usage
- Basic usage
- User guide: Connections
- Editing a track's plot as text
- Highlights
- Installing plugins
- Opening track hubs by URL
Track types
- User guide: Alignments track
- GC content track
- Gene track
- GWAS / Manhattan track
- User guide: Hi-C track
- User guide: MAF track
- Multi-row feature track
- Multi-sample variant display
- User guide: Quantitative track
- Sequence track
- User guide: Variant track
Views
- Circular genome view
- Dotplot view
- Graph genome view
- Linear synteny view
- Spreadsheet view
- SV inspector view
Sequence tools
Analysis
Tutorials
genomes.jbrowse.org
- Basic usage of genomes.jbrowse.org
- Synteny on genomes.jbrowse.org
- Proteins on genomes.jbrowse.org
- RepeatMasker as one row per class
Synteny & comparative genomics
Whole-genome alignments
- Synteny visualization (pairwise minimap2)
- Comparing one genome's two haplotypes (T2T-HG002)
- Synteny from liftOver chains (hg38 and eight vertebrates)
- Synteny visualization (all-vs-all minimap2)
- Rearrangements between genomes by type (SyRI)
- Synteny on a circle (human and mouse)
Ortholog tables
- Synteny from MCScan anchors (grape, peach)
- Synteny from an ortholog table (grape, peach, cacao)
- Synteny visualization (OrthoFinder orthogroups)
- Synteny from gene symbols (eight primates)
- Synteny from gene symbols (44 E. coli genomes)
- Synteny by ancestral linkage group (sponge, comb jelly, jellyfish)
- Selection pressure between two genomes (dN/dS)
- Synteny visualization (a polyploid against itself)
Pangenomes
- Pangenome (pggb)
- Pangenome (Minigraph-Cactus)
- Pangenome (hosting your own graph)
- Pangenome (mouse)
- Pangenome (cattle)
HPRC release 2
- Pangenome (HPRC) part 1: the graph's alleles and the haplotypes that have them
- Pangenome (HPRC) part 2: haplotypes against each other
- Pangenome (HPRC) part 3: repeat lengths across haplotypes
Structural variation
- CNV across a population (1000 Genomes)
- Structural variants (1000 Genomes)
- Structural variants from Hi-C
- Low-mappability regions (SMN)
Cancer genomics
- Complex rearrangements and derivative alleles
- Gene fusion calls and the DNA behind them
- Reviewing a whole SV callset
- Structural variants (Cancer GIAB)
- Mutation cohort (TCGA)
- CNV cohort (TCGA)
Population genomics
- Selection scans (Drosophila DGRP)
- Phased trio analysis (1000 Genomes)
- LD at a selective sweep (human)
- LD across an inversion (mosquitoes)
- QTL mapping (BXD mice)
Dog10K
- A selected haplotype (Dog10K)
- A loss-of-function allele across breeds (Dog10K)
- Structural variants (Dog10K)
- Local ancestry (Dog10K)
Epigenomics & single cell
- Methylation (long-read)
- Methylation (bisulfite)
- ChromHMM chromatin states
- Single-cell ATAC pseudobulk
- Single-cell RNA pseudobulk
- AlphaGenome predictions
Transcriptomics & proteins
Genes & annotation
- Reviewing a gene prediction (Tiberius)
- Gene density and transposon density along a chromosome
- A map of the human mitochondrial genome
Grammar of graphics
- A grammar of graphics over a BED (RepeatMasker Alu age)
- A grammar of graphics over a BAM (NA12878 insert size)