SHOREmap
To dramatically speed up identification of causative point mutations and small deletions from pooled and sequenced mapping populations, we provide the software package SHOREmap, an extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. SHOREmap requires aligned sequence data from a pooled mapping population. Based on the read count at marker positioning distinguishing the parents it regonizes regions with skews in the allele distribution. Annotating the changes within this interval rapidly leads to causal changes.
Downloads
| Release | Date | Download | Manual |
|---|---|---|---|
| Release 2.1 | 2013-08-01 | SHOREmap 2.1 | Manual |
| Release 2.0 | 2011-05-18 | SHOREmap_release_2.0.tar.gz | Manual |
| Release 1.2 | 2011-01-19 | SHOREmap_release_1.2.tar.gz In combination with SHORE version 0.4.1. or higher | Manual (r1.1) |
| 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 |
Projects
| Project description | Read data | Publication |
|---|---|---|
| Resequencing data of a pool of 500 F2 recombinants of a cross between A. thaliana Col-0 and Ler-1 selected for slow growth and light leaves. | Schneeberger.2009.single_end.gz | Schneeberger et al, 2009, Nature Methods |
| Resequencing data of a pool of 200 F2 recombinants of a cross between A. thaliana Col-0 and Ler-1 selected for late flowering. | Galvao.2012.reads1.fq.gz Galvao.2012.reads2.fq.gz | Galvao et al, 2012, Plant Journal |
| Resequencing data of a pool of 270 F2 isogenic recombinants within the background of A. thaliana Col-0 selected for suppression of lhp1 mutant phenotype. | Hartwig.2012.suppressor.reads1.fq.gz Hartwig.2012.suppressor.reads2.fq.gz Hartwig.2012.background.reads1.fq.gz Hartwig.2012.background.reads2.fq.gz | Hartwig et al, 2012, under review |
Related publication
Contact
If you have any questions, don't hesitate to contact us: Korbinian Schneeberger.