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
• Highlights
• Opening track hubs by URL
• Plugin store

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#

• BLAT and in-silico PCR
• Consensus sequence
• Feature sequence panel
• Sequence search

Analysis#

• Clustering rows
• SV visualization

Tutorials#

genomes.jbrowse.org#

• Basic usage of genomes.jbrowse.org
• Synteny on genomes.jbrowse.org
• Proteins on genomes.jbrowse.org
• RepeatMasker as one lane per class
• The HPRC pangenome on genomes.jbrowse.org

Synteny & comparative genomics#

• Synteny visualization (pairwise minimap2)
• Synteny from an ortholog table (grape, peach, cacao)
• Synteny visualization (all-vs-all minimap2)
• Rearrangements between genomes by type (SyRI)
• Comparing one genome's two haplotypes (T2T-HG002)
• Synteny between neighbouring haplotypes (the amylase locus)
• Driving JBrowse with an AI agent (two Drosophila genomes)
• Selection pressure between two genomes (dN/dS)
• Synteny by ancestral linkage group (sponge, comb jelly, jellyfish)
• Synteny from a pangenome graph (eight HPRC haplotypes)
• Synteny from gene symbols (44 E. coli genomes)
• Synteny from gene symbols (eight primates)
• Synteny from liftOver chains (hg38 and eight vertebrates)
• Synteny from MCScan anchors (grape, peach)
• Synteny on a circle (human and mouse)
• Synteny visualization (a polyploid against itself)
• Synteny visualization (OrthoFinder orthogroups)

Pangenomes#

• Pangenome (pggb)
• Pangenome (Minigraph-Cactus)
• Pangenome (HPRC) part 1, reading the graph
• Pangenome (HPRC) part 2, who carries what
• Pangenome (HPRC) part 3, every haplotype in its own coordinates
• Pangenome (HPRC) part 4, the graph as the picture
• Pangenome (HPRC) part 6, mitochondrial lineages from the graph
• Pangenome (mouse)
• Pangenome (cattle)
• Pangenome (preparing your own graph)
• Pangenome (HPRC) part 5, repeat lengths across haplotypes

Structural variation#

• Structural variants (1000 Genomes)
• CNV across a population (1000 Genomes)
• Low-mappability regions (SMN)
• Structural variants (Dog10K)
• Structural variants from Hi-C

Cancer genomics#

• Structural variants (Cancer GIAB)
• CNV cohort (TCGA)
• Complex rearrangements and derivative alleles
• Gene fusion calls and the DNA behind them
• Mutation cohort (TCGA)
• Reviewing a whole SV callset

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)
• A loss-of-function allele across breeds (Dog10K)
• A selected haplotype (Dog10K)
• Local ancestry (Dog10K)

Epigenomics & single cell#

• Methylation (long-read)
• Methylation (bisulfite)
• ChromHMM chromatin states
• Single-cell ATAC pseudobulk
• AlphaGenome predictions
• Single-cell RNA pseudobulk

Transcriptomics & proteins#

• RNA-seq visualization
• Differential transcript usage
• TP53 from prediction to crystal

Genes & annotation#

• Reviewing a gene prediction (Tiberius)

Grammar of graphics#

• A grammar of graphics over a BED (RepeatMasker Alu age)
• A grammar of graphics over a BAM (NA12878 insert size)

Configuration & embedding#

• Display settings
• Embedding JBrowse
• JBrowse CLI with Desktop
• Gene density and transposon density along a chromosome