Config guide

Intro to the config.json

A JBrowse 2 configuration file, a config.json, is structured as follows

{
  "configuration": {
    /* global configs here */
  },
  "assemblies": [
    /* list of assembly configurations, e.g. the genomes being viewed */
  ],
  "tracks": [
    /* array of tracks being loaded, contain reference to which assembl(y/ies)
    they belong to */
  ],
  "aggregateTextSearchAdapters": [
    /* optional array of text search adapters */
  ],
  "defaultSession": {
    /* optional default session */
  }
}

The most important thing to configure are your assemblies and your tracks

Configuring assemblies

An assembly configuration includes the "name" of your assembly, any "aliases" that might be associated with that assembly e.g. GRCh37 is sometimes seen as an alias for hg19, and then a "sequence" configuration containing a reference sequence track config. This is provides a special "track" that is outside the normal track config

Here is a complete config.json file containing only a hg19

{
  "assemblies": [
    {
      "name": "hg19",
      "aliases": ["GRCh37"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hg19_config",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        },
        "rendering": {
          "type": "DivSequenceRenderer"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ]
}

Configuring reference name aliasing

Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly

The refNameAliases in the above config provides this functionality

"refNameAliases": {
  "adapter": {
    "type": "RefNameAliasAdapter",
    "location": {
      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt",
      "locationType": "UriLocation"
    }
  }
}

The hg19_aliases then is a tab delimited file that looks like this

The first column should be the names that are in your FASTA sequence, and the rest of the columns are aliases

1   chr1
2   chr2
3   chr3
4   chr4
5   chr5
6   chr6
7   chr7
8   chr8
9   chr9
10  chr10
11  chr11
12  chr12
13  chr13
14  chr14
15  chr15
16  chr16
17  chr17
18  chr18
19  chr19
20  chr20
21  chr21
22  chr22
X   chrX
Y   chrY
M   chrM    MT

Adding an assembly with the CLI

Generally we add a new assembly with the CLI using something like

# use samtools to make a fasta index for your reference genome
samtools faidx myfile.fa

# install the jbrowse CLI
npm install -g @jbrowse/cli

# add the assembly using the jbrowse CLI, this will automatically copy the
myfile.fa and myfile.fa.fai to your data folder at /var/www/html/jbrowse2
jbrowse add-assembly myfile.fa --load copy --out /var/www/html/jbrowse2

See our CLI docs for the add-assembly for more details here -- add-assembly

Note: assemblies can also be added graphically using the assembly manager when you are using the admin-server. See the quickstart guide for more details.

Assembly config

Because JBrowse 2 can potentially have multiple assemblies loaded at once, it needs to make sure each track is associated with an assembly.

To do this, we make assemblies a special part of the config, and make sure each track refers to which genome assembly it uses

Example config with hg19 genome assembly loaded

Here is a complete config.json that has the hg19 genome loaded

{
  "assemblies": [
    {
      "name": "hg19",
      "aliases": ["GRCh37"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "refseq_track",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        },
        "rendering": {
          "type": "DivSequenceRenderer"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ]
}

The top level config is an array of assemblies

Each assembly contains

• name - a name to refer to the assembly by. each track that is related to this assembly references this name
• aliases - sometimes genome assemblies have aliases like hg19, GRCh37, b37p5, etc. while there may be small differences between these different sequences, they often largely have the same coordinates, so you might want to be able to associate tracks from these different assemblies together. The assembly aliases are most helpful when loading from a UCSC trackHub which specifies the genome assembly names it uses, so you can connect to a UCSC trackHub if your assembly name or aliases match.
• sequence - this is a complete "track" definition for your genome assembly. we specify that it is a track of type ReferenceSequenceTrack, give it a trackId, and an adapter configuration. an adapter configuration can specify IndexedFastaAdapter (fasta.fa and fasta.fai), BgzipFastaAdapter (fasta.fa.gz, fasta.fa.gz.fai, fasta.gz.gzi), ChromSizesAdapter (which fetches no sequences, just chromosome names)

ReferenceSequenceTrack

Example ReferenceSequenceTrack config, which as above, is specified as the child of the assembly section of the config

{
  "type": "ReferenceSequenceTrack",
  "trackId": "refseq_track",
  "adapter": {
    "type": "BgzipFastaAdapter",
    "fastaLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
      "locationType": "UriLocation"
    },
    "faiLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
      "locationType": "UriLocation"
    },
    "gziLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
      "locationType": "UriLocation"
    }
  },
  "rendering": {
    "type": "DivSequenceRenderer"
  }
}

BgzipFastaAdapter

A bgzip FASTA format file is generated by

bgzip -i sequence.fa
samtools faidx sequence.fa.gz

## above commands generates the following three files
sequence.fa.gz
sequence.fa.gz.gzi
sequence.fa.gz.fai

These are loaded into a BgzipFastaAdapter as follows

{
  "type": "BgzipFastaAdapter",
  "fastaLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
    "locationType": "UriLocation"
  },
  "faiLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
    "locationType": "UriLocation"
  },
  "gziLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
    "locationType": "UriLocation"
  }
}

IndexedFastaAdapter

An indexed FASTA file is similar to the above, but the sequence is not compressed

samtools faidx sequence.fa

## above commands generate the .fa and .fai files
sequence.fa
sequence.fa.fai

These are loaded into a IndexedFastaAdapter as follows

{
  "type": "IndexedFastaAdapter",
  "fastaLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa",
    "locationType": "UriLocation"
  },
  "faiLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.fai",
    "locationType": "UriLocation"
  }
}

TwoBitAdapter

The UCSC twoBit adapter is also supported. Note however that the 2bit format has a longer startup time than other adapters because there is a larger upfront parsing time.

{
  "type": "TwoBitAdapter",
  "twoBitLocation": {
    "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.2bit",
    "locationType": "UriLocation"
  }
}

Track configurations

All tracks can contain

• trackId - internal track ID, must be unique
• name - displayed track name
• assemblyNames - an array of assembly names a track is associated with, often just a single assemblyName
• category - (optional) array of categories to display in a hierarchical track selector

Example config.json containing a track config

{
  "assemblies": [
    {
      "name": "hg19",
      "aliases": ["GRCh37"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Pd8Wh30ei9R",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "repeats_hg19",
      "name": "Repeats",
      "assemblyNames": ["hg19"],
      "category": ["Annotation"],
      "adapter": {
        "type": "BigBedAdapter",
        "bigBedLocation": {
          "uri": "https://jbrowse.org/genomes/hg19/repeats.bb",
          "locationType": "UriLocation"
        }
      }
    }
  ]
}

AlignmentsTrack config

Example AlignmentsTrack config

{
  "trackId": "my_alignments_track",
  "name": "My Alignments",
  "assemblyNames": ["hg19"],
  "type": "AlignmentsTrack",
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "http://yourhost/file.bam",
      "locationType": "UriLocation"
    },
    "index": {
      "location": {
        "uri": "http://yourhost/file.bam.bai",
        "locationType": "UriLocation"
      }
    }
  }
}

BamAdapter configuration options

• bamLocation - a 'file location' for the BAM
• index: a subconfiguration schema containing
  • indexType: options BAI or CSI. default: BAI
  • location: a 'file location' of the index

Example BamAdapter config

{
  "type": "BamAdapter",
  "bamLocation": {
    "uri": "http://yourhost/file.bam",
    "locationType": "UriLocation"
  },
  "index": {
    "location": {
      "uri": "http://yourhost/file.bam.bai",
      "locationType": "UriLocation"
    }
  }
}

CramAdapter configuration options

• cramLocation - a 'file location' for the CRAM
• craiLocation - a 'file location' for the CRAI

Example CramAdapter config

{
  "type": "CramAdapter",
  "cramLocation": {
    "uri": "http://yourhost/file.cram",
    "locationType": "UriLocation"
  },
  "craiLocation": {
    "uri": "http://yourhost/file.cram.crai",
    "locationType": "UriLocation"
  }
}

HicTrack config

Example Hi-C track config

{
  "type": "HicTrack",
  "trackId": "hic",
  "name": "Hic Track",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "HicAdapter",
    "hicLocation": {
      "uri": "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic",
      "locationType": "UriLocation"
    }
  }
}

HicAdapter config

We just simply supply a hicLocation currently for the HicAdapter

{
  "type": "HicAdapter",
  "hicLocation": {
    "uri": "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic",
    "locationType": "UriLocation"
  }
}

HicRenderer config

• baseColor - the default baseColor of the Hi-C plot is red #f00, you can change it to blue so then the shading will be done in blue with #00f
• color - this is a color callback that adapts the current Hi-C contact feature with the baseColor to generate a shaded block. The default color callback function is jexl:baseColor.alpha(Math.min(1,count/(maxScore/20))).hsl().string() where it receives the count for a particular block, the maxScore over the region, and the baseColor from the baseColor config

VariantTrack config

• defaultRendering - options: 'pileup' or 'svg'. default 'svg'
• adapter - a variant type adapter config e.g. a VcfTabixAdapter

Example config

{
  "type": "VariantTrack",
  "trackId": "my track",
  "name": "My Variants",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "vcfGzLocation": {
      "uri": "http://yourhost/file.vcf.gz",
      "locationType": "UriLocation"
    },
    "index": {
      "location": {
        "uri": "http://yourhost/file.vcf.gz.tbi",
        "locationType": "UriLocation"
      }
    }
  }
}

VcfTabixAdapter configuration options

• vcfGzLocation - a 'file location' for the BigWig
• index: a subconfiguration schema containing
  • indexType: options TBI or CSI. default TBI
  • location: the location of the index

Example VcfTabixAdapter adapter config

{
  "type": "VcfTabixAdapter",
  "vcfGzLocation": {
    "uri": "http://yourhost/file.vcf.gz",
    "locationType": "UriLocation"
  },
  "index": {
    "location": {
      "uri": "http://yourhost/file.vcf.gz.tbi",
      "locationType": "UriLocation"
    }
  }
}

QuantitativeTrack config

Example QuantitativeTrack config

{
  "trackId": "my_wiggle_track",
  "name": "My Wiggle Track",
  "assemblyNames": ["hg19"],
  "type": "QuantitativeTrack",
  "adapter": {
    "type": "BigWig",
    "bigWigLocation": {
      "uri": "http://yourhost/file.bw",
      "locationType": "UriLocation"
    }
  }
}

General QuantitativeTrack options

• scaleType - options: linear, log, to display the coverage data. default: linear
• adapter - an adapter that returns numeric signal data, e.g. feature.get('score')

Autoscale options for QuantitativeTrack

Options for autoscale

• local - min/max values of what is visible on the screen
• global - min/max values in the entire dataset
• localsd - mean value +- N stddevs of what is visible on screen
• globalsd - mean value +/- N stddevs of everything in the dataset

Score min/max for QuantitativeTrack

These options overrides the autoscale options and provides a minimum or maximum value for the autoscale bar

• minScore
• maxScore

QuantitativeTrack drawing options

• inverted - draws upside down
• defaultRendering - can be density, xyplot, or line
• summaryScoreMode - options: min, max, whiskers

QuantitativeTrack renderer options

• filled - fills in the XYPlot histogram
• bicolorPivot - options: numeric, mean, none. default: numeric
• bicolorPivotValue - number at which the color switches from posColor to negColor. default: 0
• color - color or color callback for drawing the values. overrides posColor/negColor. default: none
• posColor - color to draw "positive" values. default: red
• negColor - color to draw "negative" values. default: blue
• clipColor - color to draw "clip" indicator. default: red

BigWigAdapter options

• bigWigLocation - a 'file location' for the bigwig

Example BigWig adapter config

{
  "type": "BigWig",
  "bigWigLocation": {
    "uri": "http://yourhost/file.bw",
    "locationType": "UriLocation"
  }
}

SyntenyTrack config

Example SyntenyTrack config

{
  "type": "SyntenyTrack",
  "trackId": "dotplot_track",
  "assemblyNames": ["YJM1447", "R64"],
  "name": "dotplot",
  "adapter": {
    "type": "PAFAdapter",
    "pafLocation": {
      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/yeast/YJM1447_vs_R64.paf",
      "locationType": "UriLocation"
    },
    "assemblyNames": ["YJM1447", "R64"]
  }
}

We can add a SyntenyTrack from PAF with the CLI e.g. with

jbrowse add-track myfile.paf --type SyntenyTrack --assemblyNames \
    grape,peach --load copy --out /var/www/html/jbrowse2

Advanced adapters

There are two useful adapter types that can be used for more advanced use cases, such as generating configuration for data returned by an API. These are the FromConfigAdapter and FromConfigSequenceAdapter. They can be used as the adapter value for any track type.

FromConfigAdapter

This adapter can be used to generate features directly from values stored in the configuration.

Example FromConfigAdapter

{
  "type": "FromConfigAdapter",
  "features": [
    {
      "refName": "ctgA",
      "uniqueId": "alias1",
      "aliases": ["A", "contigA"]
    },
    {
      "refName": "ctgB",
      "uniqueId": "alias2",
      "aliases": ["B", "contigB"]
    }
  ]
}

FromConfigSequenceAdapter

Similar behavior to FromConfigAdapter, with a specific emphasis on performance when the features are sequences.

Example FromConfigSequenceAdapter

{
  "type": "FromConfigSequenceAdapter",
  "features": [
    {
      "refName": "SEQUENCE_1",
      "uniqueId": "firstId",
      "start": 0,
      "end": 33,
      "seq": "CCAAGATCTAAGATGTCAACACCTATCTGCTCA"
    },
    {
      "refName": "SEQUENCE_2",
      "uniqueId": "secondId",
      "start": 0,
      "end": 44,
      "seq": "CCGAACCACAGGCCTATGTTACCATTGGAAAGCTCACCTTCCCG"
    }
  ]
}

Text searching

Text searching is now available on JBrowse 2.

Text searching appears in two forms: per-track indexes and aggregate indexes which search across multiple tracks

Aggregate indexes may look like this

{
"aggregateTextSearchAdapters": [
    {
      "type": "TrixTextSearchAdapter",
      "textSearchAdapterId": "hg19-index",
      "ixFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/hg19.ix",
        "locationType": "UriLocation"
      },
      "ixxFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/hg19.ixx",
        "locationType": "UriLocation"
      },
      "metaFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/meta.json",
        "locationType": "UriLocation"
      },
      "assemblyNames": ["hg19"]
    }
}

An example per-track config may look like this

{
  "trackId":"yourtrack",
  "name":"Track name",
  "adapter":{
    "type": "Gff3TabixAdapter",
    "gffGzLocation": { "uri":"yourfile.gff.gz",
        "locationType": "UriLocation" }
    "index":{ "location": { "uri":"yourfile.gff.gz.tbi",
        "locationType": "UriLocation" } }
  },
  "textSearching": {
    "textSearchAdapter": {
      "type": "TrixTextSearchAdapter",
      "textSearchAdapterId": "hg19-index",
      "ixFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/hg19.ix",
        "locationType": "UriLocation"
      },
      "ixxFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/hg19.ixx",
        "locationType": "UriLocation"
      },
      "metaFilePath": {
        "uri": "https://jbrowse.org/genomes/hg19/trix/meta.json",
        "locationType": "UriLocation"
      },
      "assemblyNames": ["hg19"]
    },
    "indexingAttributes": ["Name","ID"],
    "indexingFeatureTypesToExclude": ["CDS","exon"]
  }
}

Information on generating trix indexes via the cli can be found here

TrixTextSearchAdapter config

The trix search index is the current file format for name searching

It is based on the UCSC trix file format described here https://genome.ucsc.edu/goldenPath/help/trix.html

To create trix indexes you can use our command line tools. More info found at our jbrowse text-index guide. This tool will automatically generate a config like this. The config slots are described below for details

{
  "textSearchAdapter": {
    "type": "TrixTextSearchAdapter",
    "textSearchAdapterId": "gff3tabix_genes-index",
    "ixFilePath": {
      "uri": "trix/gff3tabix_genes.ix",
      "locationType": "UriLocation"
    },
    "ixxFilePath": {
      "uri": "trix/gff3tabix_genes.ixx",
      "locationType": "UriLocation"
    },
    "metaFilePath": {
      "uri": "trix/gff3tabix_genes_meta.json",
      "locationType": "UriLocation"
    }
  }
}

• ixFilePath - the location of the trix ix file
• ixxFilePath - the location of the trix ixx file
• metaFilePath - the location of the metadata json file for the trix index

JBrowse1TextSearchAdapter config

This is more uncommon, but allows back compatibility with a jbrowse 1 names index created by generate-names.pl

{
  "textSearchAdapter": {
    "type": "JBrowse1TextSearchAdapter",
    "textSearchAdapterId": "generate-names-index",
    "namesIndexLocation": {
      "uri": "/names",
      "locationType": "UriLocation"
    }
  }
}

• namesIndexLocation - the location of the JBrowse1 names index data directory

DotplotView config

The configuration of a view is technically a configuration of the "state of the view" but it can be added to the defaultSession

An example of a dotplot config can help explain. This is relatively advanced so let's look at an example

{
  "assemblies": [
    {
      "name": "grape",
      "sequence": {
        "trackId": "grape_seq",
        "type": "ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "grape.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "peach",
      "sequence": {
        "trackId": "peach_seq",
        "type": "ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "peach.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "trackId": "grape_peach_synteny_mcscan",
      "type": "SyntenyTrack",
      "assemblyNames": ["peach", "grape"],
      "trackIds": [],
      "renderDelay": 100,
      "adapter": {
        "mcscanAnchorsLocation": {
          "uri": "grape.peach.anchors",
          "locationType": "UriLocation"
        },
        "subadapters": [
          {
            "type": "NCListAdapter",
            "rootUrlTemplate": {
              "uri": "https://jbrowse.org/genomes/synteny/peach_gene/{refseq}/trackData.json",
              "locationType": "UriLocation"
            }
          },
          {
            "type": "NCListAdapter",
            "rootUrlTemplate": {
              "uri": "https://jbrowse.org/genomes/synteny/grape_gene/{refseq}/trackData.json",
              "locationType": "UriLocation"
            }
          }
        ],
        "assemblyNames": ["peach", "grape"],
        "type": "MCScanAnchorsAdapter"
      },
      "name": "Grape peach synteny (MCScan)",
      "category": ["Annotation"]
    },
    {
      "trackId": "grape_peach_paf",
      "type": "SyntenyTrack",
      "name": "Grape vs Peach (PAF)",
      "assemblyNames": ["peach", "grape"],
      "adapter": {
        "type": "PAFAdapter",
        "pafLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/peach_grape.paf",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "dotplot_track_small",
      "name": "Grape vs peach small (PAF)",
      "assemblyNames": ["grape", "peach"],
      "adapter": {
        "type": "PAFAdapter",
        "pafLocation": {
          "uri": "peach_grape_small.paf",
          "locationType": "UriLocation"
        },
        "assemblyNames": ["peach", "grape"]
      }
    }
  ],
  "defaultSession": {
    "name": "Grape vs Peach (small)",
    "views": [
      {
        "id": "MiDMyyWpp",
        "type": "DotplotView",
        "assemblyNames": ["peach", "grape"],
        "hview": {
          "displayedRegions": [],
          "bpPerPx": 100000,
          "offsetPx": 0
        },
        "vview": {
          "displayedRegions": [],
          "bpPerPx": 100000,
          "offsetPx": 0
        },
        "tracks": [
          {
            "type": "SyntenyTrack",
            "configuration": "dotplot_track_small",
            "displays": [
              {
                "type": "DotplotDisplay",
                "configuration": "dotplot_track_small-DotplotDisplay"
              }
            ]
          }
        ],
        "displayName": "Grape vs Peach dotplot"
      }
    ]
  }
}

Note that configuring the dotplot involves creating a "defaultSession"

Users can also open synteny views using the File->Add->Dotplot view workflow, and create their own synteny view outside of the default configuration

LinearSyntenyView config

Currently, configuring synteny is made by pre-configuring a session in the view and adding synteny tracks

{
  "defaultSession": {
    "name": "Grape vs Peach Demo",
    "drawerWidth": 384,
    "views": [
      {
        "type": "LinearSyntenyView",
        "id": "test1",
        "headerHeight": 44,
        "datasetName": "grape_vs_peach_dataset",
        "tracks": [
          {
            "type": "SyntenyTrack",
            "configuration": "grape_peach_synteny_mcscan",
            "displays": [
              {
                "configuration": "grape_peach_synteny_mcscan-LinearSyntenyDisplay",
                "height": 100,
                "type": "LinearSyntenyDisplay"
              }
            ]
          }
        ],
        "height": 400,
        "displayName": "Grape vs Peach",
        "trackSelectorType": "hierarchical",
        "views": [
          {
            "type": "LinearGenomeView",
            "id": "test1_1",
            "offsetPx": 28249,
            "bpPerPx": 1000,
            "displayedRegions": [
              {
                "refName": "Pp01",
                "assemblyName": "peach",
                "start": 0,
                "end": 100000000
              }
            ],
            "tracks": [
              {
                "type": "FeatureTrack",
                "configuration": "peach_genes",
                "displays": [
                  {
                    "configuration": "peach_genes_linear",
                    "height": 100,
                    "type": "LinearBasicDisplay"
                  }
                ]
              }
            ],
            "hideControls": false,
            "hideHeader": true,
            "hideCloseButton": true,
            "trackSelectorType": "hierarchical"
          },
          {
            "type": "LinearGenomeView",
            "id": "test1_2",
            "offsetPx": 0,
            "bpPerPx": 1000,
            "displayedRegions": [
              {
                "refName": "chr1",
                "assemblyName": "grape",
                "start": 0,
                "end": 100000000
              }
            ],
            "tracks": [
              {
                "type": "FeatureTrack",
                "configuration": "grape_genes",
                "displays": [
                  {
                    "configuration": "grape_genes_linear",
                    "height": 100,
                    "type": "LinearBasicDisplay"
                  }
                ]
              }
            ],
            "hideControls": false,
            "hideHeader": true,
            "hideCloseButton": true,
            "trackSelectorType": "hierarchical"
          }
        ]
      }
    ],
    "widgets": {},
    "activeWidgets": {},
    "connections": {}
  },
  "assemblies": [
    {
      "name": "grape",
      "sequence": {
        "trackId": "grape_seq",
        "type": "ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "grape.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "peach",
      "sequence": {
        "trackId": "peach_seq",
        "type": "ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "peach.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "trackId": "grape_peach_synteny_mcscan",
      "type": "SyntenyTrack",
      "assemblyNames": ["peach", "grape"],
      "trackIds": [],
      "renderDelay": 100,
      "adapter": {
        "mcscanAnchorsLocation": {
          "uri": "grape.peach.anchors",
          "locationType": "UriLocation"
        },
        "subadapters": [
          {
            "type": "NCListAdapter",
            "rootUrlTemplate": {
              "uri": "https://jbrowse.org/genomes/synteny/peach_gene/{refseq}/trackData.json",
              "locationType": "UriLocation"
            }
          },
          {
            "type": "NCListAdapter",
            "rootUrlTemplate": {
              "uri": "https://jbrowse.org/genomes/synteny/grape_gene/{refseq}/trackData.json",
              "locationType": "UriLocation"
            }
          }
        ],
        "assemblyNames": ["peach", "grape"],
        "type": "MCScanAnchorsAdapter"
      },
      "name": "Grape peach synteny (MCScan)",
      "category": ["Annotation"]
    },
    {
      "trackId": "peach_genes",
      "type": "FeatureTrack",
      "assemblyNames": ["peach"],
      "name": "mcscan",
      "category": ["Annotation"],
      "adapter": {
        "type": "NCListAdapter",
        "rootUrlTemplate": {
          "uri": "https://jbrowse.org/genomes/synteny/peach_gene/{refseq}/trackData.json",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "peach_genes_linear",
          "renderer": {
            "type": "PileupRenderer"
          }
        }
      ]
    },
    {
      "trackId": "peach_genes2",
      "type": "FeatureTrack",
      "assemblyNames": ["peach"],
      "name": "mcscan2",
      "category": ["Annotation"],
      "adapter": {
        "type": "NCListAdapter",
        "rootUrlTemplate": {
          "uri": "https://jbrowse.org/genomes/synteny/peach_gene/{refseq}/trackData.json",
          "locationType": "UriLocation"
        }
      }
    },
    {
      "trackId": "grape_genes",
      "type": "FeatureTrack",
      "name": "mcscan",
      "assemblyNames": ["grape"],
      "category": ["Annotation"],
      "adapter": {
        "type": "NCListAdapter",
        "rootUrlTemplate": {
          "uri": "https://jbrowse.org/genomes/synteny/grape_gene/{refseq}/trackData.json",
          "locationType": "UriLocation"
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "grape_genes_linear",
          "renderer": {
            "type": "PileupRenderer"
          }
        }
      ]
    },
    {
      "trackId": "grape_genes2",
      "type": "FeatureTrack",
      "name": "mcscan2",
      "category": ["Annotation"],
      "assemblyNames": ["grape"],
      "adapter": {
        "type": "NCListAdapter",
        "rootUrlTemplate": {
          "uri": "https://jbrowse.org/genomes/synteny/grape_gene/{refseq}/trackData.json",
          "locationType": "UriLocation"
        }
      }
    }
  ],
  "configuration": {}
}

Configuring the theme

Color

The color scheme as well as some sizing options can be configured via the theme. This is done via a top-level configuration in the config file. For example:

{
  "configuration": {
    "theme": {
      "palette": {
        "primary": {
          "main": "#4400a6"
        }
      }
    }
  }
}

JBrowse uses 4 colors that can be changed. For example, this is the default theme:

Figure: Example screenshot showing the default theme

Figure: Example screenshot showing the customized theme

The customized theme screenshot uses the below configuration

	Color code	Color
Primary	#311b92	Deep purple
Secondary	#0097a7	Cyan
Tertiary	#f57c00	Orange
Quaternary	#d50000	Red

{
  "configuration": {
    "theme" :{
      "palette": {
        "primary": {
          "main": "#311b92"
        },
        "secondary": {
          "main": "#0097a7"
        },
        "tertiary": {
          "main": "#f57c00"
        },
        "quaternary": {
          "main": "#d50000"
        }
      }
    }
  }

Logo

It is also possible to supply a custom logo to be displayed in the top right corner of the app instead of the JBrowse 2 logo. To do this, store a SVG file containing your logo on your server, and specify the path in your configuration:

{
  "configuration": {
    "logoPath": {
      "uri": "path/to/my/custom-logo.svg"
    }
  }
}

The dimensions of the logo should be 150x48px.

Sizing

You can also change some sizing options by specifying the "typography" (to change font size) and "spacing" (to change the amount of space between elements) options:

{
  "theme": {
    "typography": { "fontSize": 10 },
    "spacing": 2
  }
}

Advanced

JBrowse uses Material-UI for its theming. You can read more about Material-UI themes here. Generally, most options you could pass to Material-UI's createMuiTheme should work in the theme configuration.

Disabling analytics

This is done via adding a field in the global configuration in the config file. For example:

{
  "configuration": {
    "disableAnalytics": true
  }
}

Configuration callbacks

We use Jexl (see https://github.com/TomFrost/Jexl) for defining configuration callbacks.

An example of a Jexl configuration callback might look like this

"color": "jexl:get(feature,'strand')==-1?'red':'blue'"

The notation get(feature,'strand') is the same as feature.get('strand') in javascript code.

We have a number of other functions such as

Feature operations - get

jexl:get(feature,'start') // start coordinate, 0-based half open
jexl:get(feature,'end') // end coordinate, 0-based half open
jexl:get(feature,'refName') // chromosome or reference sequence name
jexl:get(feature,'CIGAR') // BAM or CRAM feature CIGAR string
jexl:get(feature,'seq') // BAM or CRAM feature sequence
jexl:get(feature,'type') // feature type e.g. mRNA or gene

Feature operations - getTag

The getTag function smooths over slight differences in BAM and CRAM features to access their tags

jexl:getTag(feature, 'MD') // fetches MD string from BAM or CRAM feature
jexl:getTag(feature, 'HP') // fetches haplotype tag from BAM or CRAM feature

String functions

jexl:charAt('abc',2) // c
jexl:charCodeAt(' ',0) // 32
jexl:codePointAt(' ',0) // 32
jexl:startsWith('kittycat','kit') // true
jexl:endsWith('kittycat','cat') // true
jexl:padStart('cat', 8, 'kitty') // kittycat
jexl:padEnd('kitty', 8, 'cat') // kittycat
jexl:replace('kittycat','cat','') // kitty
jexl:replaceAll('kittycatcat','cat','') // kitty
jexl:slice('kittycat',5) // cat
jexl:substring('kittycat',0,5) // kitty
jexl:trim('  kitty ') // kitty, whitespace trimmed
jexl:trimStart('  kitty ') // kitty, starting whitespace trimmed
jexl:trimEnd('  kitty ') // kitty, ending whitespace trimmed
jexl:toUpperCase('kitty') // KITTY
jexl:toLowerCase('KITTY') // kitty
jexl:split('KITTY KITTY', ' ') // ['KITTY', 'KITTY']

Math functions

jexl:max(0,2)
jexl:min(0,2)
jexl:sqrt(4)
jexl:ceil(0.5)
jexl:floor(0.5)
jexl:round(0.5)
jexl:abs(-0.5)
jexl:log10(50000)
jexl:parseInt('2')
jexl:parseFloat('2.054')

Console logging

jexl:log(feature) // console.logs output and returns value
jexl:cast({'mRNA':'green','pseudogene':'purple'})[get(feature,'type')] // returns either green or purple depending on feature type

Binary operators

jexl:get(feature,'flags')&2 // bitwise and to check if BAM or CRAM feature flags has 2 set