SHOREmap statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SHOREmap
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Tool usage distribution map

This map represents all the scientific publications referring to SHOREmap per scientific context
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Protocols

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

Versioning


No version available

Publication for SHOREmap

SHOREmap citations

 (45)
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Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development

2018
PMCID: 5873925
PMID: 29487187
DOI: 10.1534/g3.118.300496
call_split See protocol

[…] 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 (). […]

library_books

Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea) Using QTL seq Reveals Markers for Marker Assisted Selection

2018
Front Plant Sci
PMCID: 5807350
PMID: 29459876
DOI: 10.3389/fpls.2018.00083

[…] orphism (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 and fi […]

library_books

Efficient Identification of Causal Mutations through Sequencing of Bulked F2 from Two Allelic Bloomless Mutants of Sorghum bicolor

2018
Front Plant Sci
PMCID: 5771210
PMID: 29379518
DOI: 10.3389/fpls.2017.02267

[…] (Schneeberger 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 populatio […]

call_split

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

2017
Front Plant Sci
PMCID: 5615928
PMID: 29018463
DOI: 10.3389/fpls.2017.01650
call_split See protocol

[…] 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 polym […]

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Actin filament reorganisation controlled by the SCAR/WAVE complex mediates stomatal response to darkness

2017
New Phytol
PMCID: 5519931
PMID: 28636198
DOI: 10.1111/nph.14655
call_split See protocol

[…] 10 reference 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 variant […]

library_books

Arabidopsis ALA1 and ALA2 Mediate RNAi Based Antiviral Immunity

2017
Front Plant Sci
PMCID: 5383662
PMID: 28439275
DOI: 10.3389/fpls.2017.00422

[…] sive mutation. In order to map the ENOR1 locus, we generated a bulked pool of susceptible plants from the F2 population for whole-genome sequencing, screened mutations by comparing the sequences with SHOREmap methods (; ), and mapped the ENOR1 locus using CAPS markers (Figure ). We finally found that only a C to T mutation at the 2965th bp of CDS of AT5G04930, which causes a premature stop codon a […]


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