You can also download portable version of Digenome-seq!

To download and run Digenome-seq, please follow below instructions.



In order to find start/end positions of aligned sequences, 1.find_position_bam.cpp needs to be compiled into binary. By running , it will firstly automatically download and compile bamtools library ( and secondly compile 1.find_position_bam.cpp into binary. To build bamtools library properly, cmake, g++, and git should be pre-installed.


Set an environment variable 'DIGENOME_HOME', to the directory which contains python files and executables.


Copy digenome-run script to bin directory (i.e. ~/bin), and run the script to analyze BAM file, as below:

STEP 4 - Usage

Before running digenome-seq, please type digenome-run -h or --help for help message.

digenome-run [-h] [-p PREFIX] [-r RATIO_CUTOFF] [-c COUNT_CUTOFF] [-u RANGE_SUM] [-s {1,2,3,4,5,6,7,8,9,10}] [-o OVERHANG] bam_file_path

It will automatically execute all required processes. It needs 'pysam' python package and 'pypy' to run properly.

STEP 5 - Usage for advanced users

You can start from any intermediate step to the last step. For example, if you want to run step 5~10, type command:

digenome-run -s 5 bam_file_path

Additionally, you can download the source code of each step in Github(