Software

SHORE

Analysis suite for Illumina short read data.

We started the open beta testing program.

Releases:

Release 0.2.3beta, README
Release 0.2.2beta, README

Known bugs in the current release:

Run statistics show (wrong) high error rate in low-fold sequencing projects (~ less than 5 fold sequence coverage)
Correction of SNP calls for close-by polymorphic regions is not working. This could create false positive variant calls. (Thanks to Naveed Ishaque for his SHORE versus MAQ comparison.)
Viz bug. SHORE needs R scripts for plotting. Please download this file: Plot_scripts.tar.gz. Save it the folder specified in your SHORE environmental variable and un-pack it there.

Thanks to:

Colin Davenport for reporting bugs in ifastq2flat and the missing R scripts.

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

Related publication:

Ossowski S, Schneeberger K, Clark RM et al. Sequencing of natural strains of Arabidopsis thaliana with short reads, Genome Research, DOI: 10.1101/gr.080200.108

GenomeMapper

Short read mapping tool.

Releases:

Release 0.1.1beta, source code including documentation
Release 0.1beta, source code including documentation

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

POLYMORPH

Availability postponed to November 2008

Used by the 1001genomes project.

POLYMORPH is a web application for visualization and analysis of polymorphism data.

Data

1001 Genomes analysed data

Browse all data here.

Publication related data

Ossowski, S., Schneeberger, K., Clark, R. M., Lanz, C., and Weigel, D. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res., published online September 25.