• Documentation See https://github.com/grenaud/freeIbis/ for a detailed description and our wiki (https://github.com/grenaud/freeIbis/wiki) documentation.

• INSTALLATION

In the same folder as this README, there are also three other folders, run the following commands:

$ make

This should build the required binaries for freeIbis. Be sure you have bgzip (http://samtools.sourceforge.net/tabix.shtml ) installed and in your path as freeIbis requires this to generate bam files. Try typing "bgzip -h" to see if it works.

You may now edit params.py in the current directory to change default values. In most cases this is not necessary, however if your /tmp folder does not have at least 30 Gb free disk space, you should use another default temp folder.

Base calling should typically be started using

./runBaseCalling.py

This should give you the list of options. Ideally, you will only need a few of them. However, you should check the website above for details.

Enjoy using freeIbis.