SHORE protocols

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SHORE specifications

Information


Unique identifier OMICS_01136
Name SHORE
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
Wikipedia http://shore.sourceforge.net/wiki/

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Maintainers


  • person_outline Stephan Ossowski <>
  • person_outline Detlef Weigel <>

Publication for SHORE

SHORE in pipelines

 (3)
2016
PMCID: 4844672
PMID: 27097556
DOI: 10.1038/ncomms11222

[…] prepared using standard illumina protocols. deep sequencing was performed on an illumina gaiix instrument following the manufacturer's instructions., bioinformatics analyses were performed using the shore suite (version 0.9.3) (ref. ) and scripts in python (version 2.7.3) using biopython (version 1.60), pybedtools (version 0.6.4) and matplotlib (version 1.2.0) modules. all statistical analyses […]

2014
PMCID: 4230842
PMID: 25393550
DOI: 10.1371/journal.pgen.1004785

[…] twelve different samples in each lane. each pool was sequenced over three lanes. the illumina rta software (version 1.13.48) performed image analysis and base calling., reads were trimmed using the shore import function in shore version 0.9.0 . command line arguments can be found in . this function simultaneously trims reads and separates samples by barcode. since all samples were sequenced […]

2012
PMCID: 3441220
PMID: 22899815
DOI: 10.1186/1471-2164-13-393

[…] the reads was performed using the open source short read aligner bowtie (release 0.12.5) [] and limited to 2 mismatches. homozygous and heterozygous snps were identified using the freeware package shore []. samples were concurrently analyzed by agrf qld using casava software (version 1.7, illumina inc. san diego, ca, usa) to identify snps. both approaches yielded the same result. biological […]


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SHORE in publications

 (27)
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 […]

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, […]

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; […]

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 filterpcrdupl.pl script (version 1.01) included in condetri version 2.0 […]

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 […]


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

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