Shord read mapping and analysis pipeline.

SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform. It allows the incorporation of different aligners, and its different modules support a range of experiments, such as resequencing, mapping of mutants, ChIP-seq analyses and several more.


SHORE is now hosted on sourceforge. We provide source code and precompiled binaries.
Find SHORE here:

Read the manual here:

Related publication

Sequencing of natural strains of Arabidopsis thaliana with short reads
Ossowski S., Schneeberger K., Clark R. M., Lanz C., Warthmann N. and Weigel D.
Genome Res (2008), 18(12) 2024-33.


If you have any questions, don't hesitate to contact us: Stephan Ossowski or Jörg Hagmann.