This folder contains the data and the results discussed in the paper entitled 
"Pangenomics read mapping", and scripts to reproduce the results. 
Data and results are organized in directories by experiment. 

229M	exp1.tgz
3.4G	exp2.tgz
5.0G	exp3.tgz
39G	exp4.tgz
G	exp5.tgz
101	pantools.tgz

Compressed files for each directory can be downloaded from
www.bioinformatics.nl/pangenomics.  Note that pre-created PanTools databases
are included, but generally not raw data; README files are provided with
instructions on where to download and store these.  In case of issues with
downloading or running, contact Sandra Smit (Sandra.Smit@wur.nl).

REQUIREMENTS

Scripts require Python 2.x to be installed.

Unpack pantools.tgz in your home directory (the scripts use
~/pantools/pantools.jar) - or elsewhere and change the scripts accordingly.

Install the following binaries in the "tools" directory:
- ART:		art_illumina, v2.5.8
- SAMTools:	samtools, v0.1.19-96b5f2294a
- Bowtie2: 	bowtie2, v2.2.6 	(in a subdirectory bowtie2)
- BWA:		bwa, v0.7.17-r1188	(in a subdirectory bwa)
- NextGenMap:	ngm, v0.5.0		(in a subdirectory ngm)
- Stampy:	stampy.py, v1.0.31	(in a subdirectory stampy)