Genome

In igv.js a genome refers to a reference sequence and, optionally, one or more associated tracks and metadata such as chromosome aliases and chromosome cytobands.

The reference genome can be defined with either the genome or reference property. One of these options is required.

genome property#

The genome property specifies a reference genome by an identifier for either (1) an IGV hosted genome definition, or (2) a UCSC GenArk assembly.

Example - IGV hosted genome

{
  ...
  genome: "hg38",
  ...
}

Example - UCSC GenArk assembly

{
  ...
  genome: "GCA_000002305.1"
  ...
}

IGV hosts a limited number of genome assemblies, which are listed in the table below. The UCSC GenArk site hosts an extensive list of assembly hubs, currenlty numbering 4,247. The complete listing can be found here.

IGV Hosted Genomes

id	name
hs1	Human (T2T CHM13-v2.0/hs1)
chm13v1.1	Human (T2T CHM13-v1.1)
hg38	Human (GRCh38/hg38)
hg38_1kg	Human (hg38 1kg/GATK)
hg19	Human (GRCh37/hg19)
hg18	Human (hg18)
mm39	Mouse (GRCm39/mm39)
mm10	Mouse (GRCm38/mm10)
mm9	Mouse (NCBI37/mm9)
rn7	Rat (rn7)
rn6	Rat (RGCS 6.0/rn6)
gorGor6	Gorilla (Kamilah_GGO_v0/gorGor6)
gorGor4	Gorilla (gorGor4.1/gorGor4)
panTro6	Chimp (panTro6) (panTro6)
panTro5	Chimp (panTro5) (panTro5)
panTro4	Chimp (SAC 2.1.4/panTro4)
macFas5	Macaca fascicularis (macFas5)
GCA_011100615.1	Macaca fascicularis 6.0 (GCA_011100615.1)
panPan2	Bonobo (MPI-EVA panpan1.1/panPan2)
canFam3	Dog (Broad CanFam3.1/canFam3)
canFam4	Dog (UU_Cfam_GSD_1.0/canFam4)
canFam5	Dog (canFam5)
bosTau9	Cow (ARS-UCD1.2/bosTau9)
bosTau8	Cow (UMD_3.1.1/bosTau8)
susScr11	Pig (SGSC Sscrofa11.1/susScr11)
galGal6	Chicken (galGal6)
GCF_016699485.2	Gallus gallus (GCF_016699485.2)
danRer11	Zebrafish (GRCZ11/danRer11)
danRer10	Zebrafish (GRCZ10/danRer10)
ce11	C. elegans (ce11)
dm6	D. melanogaster (dm6)
dm3	D. melanogaster (dm3)
dmel_r5.9	D. melanogaster (dmel_r5.9)
sacCer3	S. cerevisiae (sacCer3)
ASM294v2	S. pombe (ASM294v2)
ASM985889v3	Sars-CoV-2 (ASM985889v3)
tair10	A. thaliana (TAIR 10)
GCA_003086295.2	Peanut (GCA_003086295.2)
GCF_001433935.1	O. sativa IRGSP-1.0 (GCF_001433935.1)
NC_016856.1	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
GCA_000182895.1	Coprinopsis cinerea okayama7#130 (GCA_000182895.1)

reference object#

To define or customize a reference genome the reference property can be used.

example#

{
  reference: {
    "id": "hg38",
    "name": "Human (GRCh38/hg38)",
    "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
    "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
    "cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
    "tracks": [
      {
        "name": "Refseq Genes",
        "url": "https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz",
        "order": 1000000,
        "indexed": false
      }
    ]
  }
}

details#

All properties except a reference sequence URL (fastaURL or twoBitURL) are optional. An index is highly recommended for fasta files if the sequence is > a few mb in size. Loading a large fasta file without an index is likely to freeze the browser. In total there are 4 options for defining the reference sequence:

1. Fasta file without index, useful for small (< 10 MB) sequences. fastaURL
2. Indexed fasta file. fastaURL, indexURL
3. BGZIPPED compressed fasta file. fastaURL, indexURL, compressedIndexURL
4. UCSC two bit sequence file (see [twobit]). (https://genome.ucsc.edu/goldenPath/help/twoBit.html). twoBitURL

Option	Description	Default
id	UCSC or other id string.
name	A descriptive name.
fastaURL	URL to a FASTA file. Either fastaURL or twoBitURL is required.
indexURL	URL to a FASTA index (.fai file). An index file is optional, but if not supplied the entire fasta is read.
compressedIndexURL	URL to a BGZIPPED compressed fasta file (.gzi index). Note this is in addition, not in place, of the .fai index.
twoBitURL	URL to a UCSC two-bit sequence file (Version 3.0). Required if fastaURL is not defined. If both fastaURL and twoBitURL are defined twoBitURL will be used for igv.js version >= 3.0, fastaURL for earlier igv.js versions.
cytobandURL	URL to a cytoband ideogram file in UCSC format. Optional
aliasURL	URL to a tab-delimited file defining aliases for chromosome names. Theformat is tab delimited with 1 line per chromosome. Each line begins with the canonical chromosome followed by aliases. See the example below. Optional
chromSizesURL	URL to a UCSC .chrom.sizes file. This can be used in combination with twoBitURL to support the whole genome view.
indexed	Flag indicating if the FASTA is indexed. Ignored if indexURL is supplied. The primary purpose of this property is to indicate that the fasta is not indexed. Deprecated as of Version 3.0
tracks	A list of tracks to be loaded with the genome. See the tracks description for details. Optional
chromosomeOrder	An array of chromosome names defining the order in the whole genome view and chromosome pulldown selector, if used. Optional
headers	HTTP headers to include with each request. For example {"authorization": "bearer: token"}. Optional
wholeGenomeView	Construct a "whole genome" view from the individual sequences. This is useful for finished assemblies with a few (< 50) large chromosomes. Its not useful for assemblies with a single or conversely thousands of sequences. Optional	true

Chromosome alias example#

Below is the contents of a chromosome alias file.

chr1    1   CM000663.2  NC_000001.11
chr2    2   CM000664.2  NC_000002.12
chr3    3   CM000665.2  NC_000003.12
chr4    4   CM000666.2  NC_000004.12
chr5    5   CM000667.2  NC_000005.10
chr6    6   CM000668.2  NC_000006.12
chr7    7   CM000669.2  NC_000007.14
chr8    8   CM000670.2  NC_000008.11
chr9    9   CM000671.2  NC_000009.12
chr10   10  CM000672.2  NC_000010.11
chr11   11  CM000673.2  NC_000011.10
chr12   12  CM000674.2  NC_000012.12
chr13   13  CM000675.2  NC_000013.11
chr14   14  CM000676.2  NC_000014.9
chr15   15  CM000677.2  NC_000015.10
chr16   16  CM000678.2  NC_000016.10
chr17   17  CM000679.2  NC_000017.11
chr18   18  CM000680.2  NC_000018.10
chr19   19  CM000681.2  NC_000019.10
chr20   20  CM000682.2  NC_000020.11
chr21   21  CM000683.2  NC_000021.9
chr22   22  CM000684.2  NC_000022.11
chrX    X   CM000685.2  NC_000023.11    23
chrY    Y   CM000686.2  NC_000024.10    24
chrM    MT  J01415.2    NC_012920.1 chrMT