SHOREmap specifications

Information


Unique identifier OMICS_05848
Name SHOREmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SHOREmap

SHOREmap in publications

 (42)
PMCID: 5873925
PMID: 29487187
DOI: 10.1534/g3.118.300496

[…] 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 ()., rna from five day old seedlings grown in 0.5x ms liquid media was prepared using rneasy plant mini kits (qiagen). it was quantified using a nanodrop nd-1000 (thermo scientific) […]

PMCID: 5807350
PMID: 29459876
DOI: 10.3389/fpls.2018.00083

[…] (aflp) and restriction fragment length polymorphism (rflp) markers (; ). this method was combined with next generation sequencing (ngs) to map mutations to functional variant resolution using shoremap (). the shoremap methodology was then extended as mapping-by-sequencing to map functional variants in non-model organisms (). finally, qtl-seq was proposed as a fast method to identify […]

PMCID: 5771210
PMID: 29379518
DOI: 10.3389/fpls.2017.02267

[…] and weigel, ). two general approaches have been developed for using ngs to identify causal mutations. the first strategy is represented by two similar approaches, mapping-by-sequencing (shoremap) (schneeberger et al., ; hartwig et al., ) and next-generation mapping (ngm) (austin et al., ). these approaches are very similar to conventional map-based cloning. first, a mapping […]

PMCID: 5615928
PMID: 29018463
DOI: 10.3389/fpls.2017.01650

[…] schneeberger et al., ). the alignments were corrected using paired-end information before polymorphism detection using shore. finally, the allele frequencies of col-0 and ler-0 were determined using shoremap (schneeberger et al., ) and the boost function was applied to determine the final mapping interval. an annotated list of all snps was obtained using shoremap after filtering out the ler […]

PMCID: 5519931
PMID: 28636198
DOI: 10.1111/nph.14655

[…] genome using bowtie2 (langmead & salzberg, ) on very sensitive settings. variants were subsequently called and the vcf files were generated using samtools (li et al., ) and bcftools. the shoremap method (schneeberger et al., ) was used to remove background ler variants, filter variants by ems type (g to a or c to t), allele frequency, read depth and mapping quality, and to map […]


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