# Add a new reference genome to the database

This manual is intended to guide you to load new reference genome(s) to the database.

# What is Reference Genome (also know as reference assembly)?

A digital nucleic acid sequence database assembled by scientists as a representative example of a species' set of genes. Reference genomes can be accessed online using dedicated browsers such as UCSC Genome Browser.

# Why does reference genomes matter?

Mutation and Segment plots on Patient View are using genomic coordinates. The cytoband column in the Mutated Gene table on Study view rely on the Genome Reference Consortium Build matching the version used to analyse the original data (before it was loaded into cBioPortal DB).

# How to load reference genome(s) to the database?

# 1. prepare a tab delimited txt file with the following fields:

  1. species: the group of organisms e.g human
  2. name: the name of reference genome as used by the UCSC browser eg. hg19
  3. build_name: the version of Genome Reference Consortium Build published by NCBI e.g GRCh38
  4. nonN_bases: the total number of non-N bases in reference genome FASTA-formatted file
  5. URL: the URL to download the reference genome
  6. release_date: when reference genome released, in a format of yyyy-mm-dd. The release date normally is included in the README.txt file in the download directory.

here is a sample reference genome file:

#species	name	build_name	nonN_bases	URL	release_date
human	hg19	GRCh37	2897310462	https://hgdownload.cse.ucsc.edu/goldenPath/hg19	2009-02-01
human	hg38	GRCh38	3049315783	https://hgdownload.cse.ucsc.edu/goldenPath/hg38	2013-12-24
mouse	mm10	GRCm38	2652783500	https://hgdownload.cse.ucsc.edu/goldenPath/mm10	2011-12-01

# 2. Using import script to load reference genome(s) data to the database:

 cd <your_cbioportal_dir>/core/src/main/scripts
 export PORTAL_HOME=<your_cbioportal_dir>
./importReferenceGenome.pl --ref-genome <your_reference_genome_file>

# 3. output of the script runs successfully

$ ./importReferenceGenome.pl --ref-genome ~/myspace/cbioportal/core/src/test/resources/reference_genomes.txt
   Reading reference genome from:  /Users/kelsyzhu/myspace/cbioportal/core/src/test/resources/reference_genomes.txt
    --> total number of lines:  3
   Done. Restart tomcat to make sure the cache is replaced with the new data.
   Warnings / Errors:
   0.  New reference genome added; 3x
   Total time:  3432 ms