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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




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  • person_outline Stephan Ossowski
  • person_outline Detlef Weigel

Publication for SHORE

SHORE citations


The rate and potential relevance of new mutations in a colonizing plant lineage

PLoS Genet
PMCID: 5825158
PMID: 29432421
DOI: 10.1371/journal.pgen.1007155

[…] kits (illumina, san diego, ca), and sequenced on illumina hiseq 2000, hiseq 2500 or miseq instruments. paired-end reads from modern samples were trimmed and quality filtered before mapping using the shore pipeline v0.9.0 [,]. because ancient dna fragments are short () we merged forward and reverse reads for herbarium samples after trimming, requiring a minimum of 11 bp overlap [], and treated […]


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

[…] 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, […]


Rapid generation of a transgene free powdery mildew resistant tomato by genome deletion

Sci Rep
PMCID: 5428673
PMID: 28352080
DOI: 10.1038/s41598-017-00578-x

[…] concentration on the flowcell was 200 pm which resulted in 2 × 329 m reads (past filter) in the first lane and 2 × 319 m reads in the second lane., each tomato line was analyzed separately with the shore pipeline, using bwa aln (v0.6.2) with option “-n 0.05” to map the reads to the solanum lycopersicum (version sl2.40.26; […]


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

[…] illumina hiseq2000 platform. see for details about library sizes and sequencing yield., all genomic libraries were retrieved and converted to fastq format using the import and convert commands in shore version 0.7.1 []. to remove pcr duplicates for a non-random fragment representation, each library was scanned with the script (version 1.01) included in condetri version 2.0 […]


UVR2 ensures transgenerational genome stability under simulated natural UV B in Arabidopsis thaliana

Nat Commun
PMCID: 5146273
PMID: 27905394
DOI: 10.1038/ncomms13522

[…] (agilent) and high-quality libraries were 100 bp paired-end-sequenced on a hiseq2500 (illumina) instrument to an average 35 × genome coverage ( and )., reads were adaptor- and quality-trimmed using shore (v8; ref. ). filtered and trimmed reads where aligned to col-0 reference sequence (tair10, 119 mbp) using genomemapper integrated in shore (v8) using a maximum of 5% of the read length […]


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

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

[…] 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 ()., to identify larger genomic regions of different allele frequencies (that is, proportion of reads for each variant found at a single single-nucleotide polymorphism […]

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

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