SHORE, SHOREmap

SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions.

Download SHORE

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

http://sourceforge.net/projects/shore/files

Contact

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

Download SHOREmap

Release	Date	Download	Manual
Release 1.1	2009-08-11	SHOREmap_release_1.1.tar.gz In combination with SHORE version 0.4.1. or higher	Manual
Release 1.0	2009-03	SHOREmap_release_1.0.tar.gz In combination with SHORE version 0.3.1 or lower	Manual

Additional files

Please note: All positions in the example files are relative to TAIR8!

For SHOREmap version 1.1 we have updated the example files, but in the same organization as described below. The large file can be found here, the small one here.

For SHOREmap version 1.0, example input and output files can be found here. Be aware that the file size is 3.4 GB, uncompressed it makes up over 40 GB. A smaller set without the SHORE base count per position file can be found here here.

The large file package including the SHORE base count per position file is required as input for testing SHOREmap INTERVAL. The smaller set is sufficient for running tests with SHOREmap DENOVO and ANNOTATE.