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Synteny track 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"
    },
    "assemblyNames": ["YJM1447", "R64"]
  }
}

We can load 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

The first assembly is the "target" and the second assembly is the "query."

See how to configure JBrowse using the CLI for more ways to load synteny tracks with the CLI.

PAFAdapter config​

The PAF adapter reflects a pairwise alignment, and is outputted by tools like minimap2. It can be used for SyntenyTracks:

{
  "type": "PAFAdapter",
  "pafLocation": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/yeast/YJM1447_vs_R64.paf"
  },
  "assemblyNames": ["YJM1447", "R64"]
}

Slots

  • pafLocation - the location of the PAF file. The pafLocation can refer to a gzipped or unzipped delta file. It will be read into memory entirely as it is not an indexed file format.
  • assemblyNames - list of assembly names, typically two (first in list is target, second is query)
  • queryAssembly - alternative to assemblyNames: just the assemblyName of the query
  • targetAssembly - alternative to assemblyNames: just the assemblyName of the target

DeltaAdapter config​

The DeltaAdapter is used to load .delta files from MUMmer/nucmer. It can be used for SyntenyTracks:

{
  "type": "DeltaAdapter",
  "deltaLocation": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/yeast/YJM1447_vs_R64.paf"
  },
  "assemblyNames": ["YJM1447", "R64"]
}

Slots

  • deltaLocation - the location of the delta file. The deltaLocation can refer to a gzipped or unzipped delta file. It will be read into memory entirely as it is not an indexed file format.
  • assemblyNames - list of assembly names, typically two (first in list is target, second is query)
  • queryAssembly - alternative to assemblyNames: just the assemblyName of the query
  • targetAssembly - alternative to assemblyNames: just the assemblyName of the target

ChainAdapter config​

The ChainAdapter is used to load .chain files from MUMmer/nucmer. It can be used for SyntenyTracks:

{
  "type": "DeltaAdapter",
  "deltaLocation": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/yeast/YJM1447_vs_R64.paf"
  },
  "assemblyNames": ["YJM1447", "R64"]
}

Slots

  • chainLocation - the location of the UCSC chain file. The chainLocation can refer to a gzipped or unzipped delta file. It will be read into memory entirely as it is not an indexed file format.
  • assemblyNames - list of assembly names, typically two (first in list is target, second is query)
  • queryAssembly - alternative to assemblyNames: just the assemblyName of the query
  • targetAssembly - alternative to assemblyNames: just the assemblyName of the target

MCScanAnchorsAdapter​

The .anchors file from MCScan refers to pairs of homologous genes and can be loaded into synteny tracks in JBrowse 2:

{
  "type": "MCScanAnchorsAdapter",
  "mcscanAnchorsLocation": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape.peach.anchors.gz"
  },
  "bed1Location": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/grape.bed.gz"
  },
  "bed2Location": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/peach.bed.gz"
  },
  "assemblyNames": ["grape", "peach"]
}

This guide shows a demonstration of how to create the anchors and bed files (the .bed files are intermediate steps in creating the anchors files and are required by the MCScanAnchorsAdapter).

Slots:

  • mcscanAnchorsLocation - the location of the .anchors file from the MCScan workflow. The .anchors file has three columns. It can be gzipped or ungzipped, and is read into memory whole
  • bed1Location - the location of the first assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "left" side of the .anchors file.
  • bed2Location - the location of the second assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "right" side of the .anchors file.

MCScanSimpleAnchorsAdapter​

The "simple" .anchors.simple file from MCScan refers to pairs of homologous genes and can be loaded into synteny tracks in JBrowse 2:

{
  "type": "MCScanSimpleAnchorsAdapter",
  "mcscanSimpleAnchorsLocation": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape.peach.anchors.simple.gz"
  },
  "bed1Location": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/grape.bed.gz"
  },
  "bed2Location": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/synteny/grape_vs_peach/peach.bed.gz"
  },
  "assemblyNames": ["grape", "peach"]
}

This guide shows a demonstration of how to create the anchors and bed files (the .bed files are intermediate steps in creating the anchors.simple files and are required by the MCScanSimpleAnchorsAdapter)

Slots:

  • mcscanSimpleAnchorsLocation - the location of the .anchors.simple file from the MCScan workflow (this file has 5 columns, start and end gene from bed1, start and end genes from bed2, and score). It can be gzipped or ungzipped, and is read into memory whole
  • bed1Location - the location of the first assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "left" side of the .anchors file.
  • bed2Location - the location of the second assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "right" side of the .anchors file.