Hosting genomes in 2bit format

[Solomon Grant]

Hello!

The documentation for the reference object only indicates fasta files as a supported format for reference genome sequences. I am interested in hosting my own genome server (as described here) to support both desktop and web-app IGV usage. I know that some of the default IGV hosted genomes include a twoBitURL parameter, apparently to support older versions of IGV. I can't find any documentation on the support for the .2bit format. When I host my own genomes is it not recommended to use the .2bit format?

Thanks,

Solomon

[igv-help]

Hi, the documentation is out of date, two bit URLs are supported.    However features that depend on knowledge of the chromosome names, such as the whole genome view,  are not supported without extra information, as the names were obtained from a fasta index file.   The easiest way to supply the chromosome names for a twoBitURL is explicitly with the chromosomeOrder property.    An example json definition follows, the cytoband and alias properties are optional.

{
"id": "hg38",
"name": "Human (GRCh38/hg38)",
"cytobandURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/cytoBandIdeo.txt.gz",
"aliasURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/hg38_alias.tab",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz",
"indexed": false,
"order": 1000001,
"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
}
],
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
}

[igv-help]

The 2bit format is fully supported in IGV desktop.  We will shortly be releasing a new version of igv.js and igv-web that has the 2bit support.