1001 Genomes
A Catalog of Arabidopsis thaliana Genetic Variation
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Related publication

Ossowski S, Schneeberger K, Clark RM et al.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.

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Schneeberger K, Ossowski S et al.
SHOREmap: simultaneous mapping and mutation identification by deep sequencing
Nature Methods 6, 550 - 551 (2009) | doi:10.1038/nmeth0809-550.

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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.

Changes in version 0.4.1beta include:

Changes in version 0.4.0beta include:

Download SHORE

Release Date Download
Release 0.4.1beta 2009-08-06 README
Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC
Release 0.4.0beta 2009-08-04 README
Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC
Release 0.3.1beta 2009-03-19 Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC
Release 0.3beta 2009-03-18 Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC
Release 0.2.4beta 2008-12-04 README
Linux, 32bit binary
Linux, 64bit binary
Release 0.2.3beta 2008-11-19 README
Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC
Release 0.2.2beta 2008-10-31 README
Linux, 32bit binary
Linux, 64bit binary
Mac OS X 10.5, Intel
Mac OS X 10.5, PPC

Issues

There are some known bugs in the current release:

Thanks to:

Contact

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


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

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.

Contact

If you have any questions, don't hesitate to contact us: Korbinian Schneeberger.