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:
- SHOREmerge with adjustable tmp folder.
Changes in version 0.4.0beta include:
- Updated variants calling, including qualities.
- New coverage analysis and segmentation algorithm.
- Customized sort algorithm making SHORE more stable.
- FastQ importer running stable.
- R scripts for visualization integrated in shore binary.
- SHORE illumina2flat improved drastically. It allows full control over all different quality values and their representation.
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:
- Run statistics show (wrong) high error rate in low-fold sequencing projects (~ less than 5 fold sequence coverage)
Thanks to:
- Colin Davenport for reporting bugs in ifastq2flat and the missing R scripts.
- Emmanuel Beaudoing for reporting a bugs and never giving up.
- Jarrod Chapman for reporting wrong settings and description in GenomeMapper.
- Ryan Lister for various bug reports.
- Ronan O'Malley for various bug reports.
- Konrad Paszklewicz for spotting a sorting problem.
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.
