Building the Cornetto C programme requires a compiler that supports C99 standard (with X/Open 7 POSIX 2008 extensions), which is widely available. To build:
sudo apt-get install zlib1g-dev #install zlib development libraries
git clone https://github.com/hasindu2008/cornetto
cd cornetto
make
The commands to zlib development libraries on some popular distributions :
On Debian/Ubuntu : sudo apt-get install zlib1g-dev
On Fedora/CentOS : sudo dnf/yum install zlib-devel
On OS X : brew install zlib
To generate the dotplot use the scripts/minidotplot.sh. This script requires minimap2, samtools.
scripts/minidotplot.sh hg002v1.0.1_pat.fasta asm.fasta
To get the telomere statistics use the scripts/telostats.sh. This script uses cornetto subcommands that implements functionality of teleomere analysis scripts from the VGP project.
scripts/telostats.sh asm.fasta
To get per-chromosome statistics use the scripts/asmstats.sh. Make sure you have already run scripts/minidotplot.sh and scripts/telostats.sh before running this script. This is because the files generated in those steps are reused by this script.
scripts/asmstats.sh asm.fasta
Our Cornetto C programme contains a number of subtools that are used by the above explained scripts. If you want to use those subtools in your scripts, see the manual page.