Building a Genome

The Mango browser requires a remote TwoBit reference file, a local gene file, and a local chromosome size file to run.

These files are downloaded from UCSC Genome Browser downloads.

Assembling a Default Genome File

To assemble a genome file, run:

./bin/make_genome <GENOME_NAME> <OUTPUT_LOCATION>

This will download required files for the genome build, compress them, and save them to <OUTPUT_LOCATION>. All builds accessible from the UCSC Downloads page are supported.

The file hg19.genome build exists in the example-files/ folder as a reference.

Assembling a Custom Genome File

If you need to assemble a custom genome file that is not supported by the make_genome executable, you can assemble one as follows.

First specify a folder, <YOUR_GENOME>.genome, and include the following files:

• cytoBand.txt: UCSC formatted cytoBand file
• <YOUR_GENOME>.chrom.sizes: tab delimited file of chromosome names and sizes
• refGene.txt: UCSC formatted tab delimited text file of gene information
• properties.txt: File containing metainformation for your genome

The properties.txt file should be formatted as follows:

sequenceLocation=http://<path_to_remote_2bit_file>.2bit
refGene=refGene.txt
chromSizes=<YOUR_GENOME>.chrom.sizes
cytoband=cytoBand.txt

Note that the sequenceLocation parameter must link to a remote TwoBit file.