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SHORE specifications


Unique identifier OMICS_01136
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Beta
Maintained Yes




No version available


  • person_outline Stephan Ossowski
  • person_outline Detlef Weigel

Publication for SHORE

SHORE citations


Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development

PMCID: 5873925
PMID: 29487187
DOI: 10.1534/g3.118.300496
call_split See protocol

[…] NEBNext DNA library prep set for Illumina (NEB) was used to prepare the sequencing library that was sequenced using an Illumina HiSeq (Illumina). Reads were mapped to the TAIR9 reference genome using SHORE and bom1 was mapped using SHOREmap (). […]


The Plant Immunity Regulating F Box Protein CPR1 Supports Plastid Function in Absence of Pathogens

Front Plant Sci
PMCID: 5615928
PMID: 29018463
DOI: 10.3389/fpls.2017.01650
call_split See protocol

[…] hich were then filtered for quality, trimmed to a minimum length of 75 bp, before aligning to the Arabidopsis thaliana reference genome, allowing for a maximum of 10% mismatches and 7% gaps using the SHORE and GenomeMapper software programs (Ossowski et al., ; Schneeberger et al., ). The alignments were corrected using paired-end information before polymorphism detection using SHORE. Finally, the […]


Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny

Front Physiol
PMCID: 5611445
PMID: 28979209
DOI: 10.3389/fphys.2017.00670

[…] regions for the 16 species not included in the Gaudry et al. () study were also examined for the presence of inactivating (e.g., splice site, frameshift, and non-sense) mutations.The PRR proposed by Shore et al. () was generally less conserved than the enhancer, often with large insertions or deletions, therefore the same annotation methods described above could not be effectively applied to this […]


The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population

PLoS One
PMCID: 5199103
PMID: 28033408
DOI: 10.1371/journal.pone.0169087

[…] ximate insert size of 120–220 bp, were sequenced single-end on an Illumina HiSeq 2000 lane.The raw reads were obtained from the sequencing platform, converted to FASTQ format and de-multiplexed using shore version 0.8.1. Read mapping was performed separately for each individual with bowtie2 version 2.1.0 []. Mapping results were enhanced by local realignment using GATK version 2.4–9 []. Single nuc […]


What causes mating system shifts in plants? Arabidopsis lyrata as a case study

PMCID: 5176122
PMID: 27804968
DOI: 10.1038/hdy.2016.99

[…] p to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as previously described (). […]


Cell adhesion in plants is under the control of putative O fucosyltransferases

PMCID: 4958334
PMID: 27317803
DOI: 10.1242/dev.132308

[…] a2-1. Illumina sequencing of pools of ∼200 backcrossed F2 suppressors per M2 suppressor line was carried out at The Genome Analysis Centre (TGAC, Norwich, UK). Sequencing data were analyzed using the SHORE () and SHOREmap () pipelines for the identification of SNPs and indels and their frequency for the bulk segregant analysis. Further details of the genetic mapping, whole-genome sequencing and th […]


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SHORE institution(s)
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany

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