Install program



Unpacking the bundle will create a directory that includes most dependencies. The executable cg must stay in this directory (it finds the dependencies based on its dir). You can use a softlink to make it available in a bin directory.

Install databases


For some analysis, such as annotation, you need several databases. These have to be available in a directory you will give as a parameter (refdir). You can download these for the hg18 and hg19 builds of the human genome:

Build databases

Optionally, the bundle contains the following scripts that can be used to download the source data and build the databases for the hg18 and hg19 builds of the human genome. This is a process that takes quite some time and space.

Most databases are originated from the UCSC genome browser tables. The databases will be automatically created in the directory /complgen/refseq/hg18 or /complgen/refseq/hg19. You can change the location by editing the script. Custom or in-house database annotations can easily be added by following the protocols described in this script.

Example files

To be able to demonstrate selected queries, we have made our annotations of the comparison of chr22 of the NA19240 individual sequenced with Illumina GAII and Complete Genomics available: NA19240_chrom22.tsv.rz. The file is compressed using the razip format that is compatible with gzip, but allows random access. A detailed description of the columns present in this file are presented here.

System Requirements

The first download is for 32bit Linux (Linux-i686), the second one for 64bit Linux (Linux-x86_64) The 32bit Linux (Linux-i686) is usually also supported on 64bit systems. A typical solution on 64bit systems can be to install the requested libraries (e.g. on Ubuntu Linux using the command sudo apt-get install ia32-libs libc6-i386 lib32gcc1) <

Binaries have been cross-compiled using gcc-4.2.0 and glibc-2.4 for compatibility (more recent glibc are backwards compatible). As glibc is not necesarily forwards-compatible, systems with older glibc may pose problems.