HighMap specifications

Information


Unique identifier OMICS_14964
Name HighMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for HighMap

HighMap in publications

 (35)
PMCID: 5883025
PMID: 29615772
DOI: 10.1038/s41598-018-23873-7

[…] of aa and bb, only the 7,949 markers that fell into the aa × bb segregation pattern were used in linkage analysis.figure 1, comparing with the reference genome (http://peanutbase.org/home), highmap assigned 2,334 of 2,384 markers to 20 lgs of peanut including 2,266 snps and 68 ssrs. the total genetic length of the molecular linkage map was 2,586.37 cm in twenty linkage groups […]

PMCID: 5880926
PMID: 29636767
DOI: 10.3389/fpls.2018.00398

[…] the filtered marker into linkage groups (lgs) based on their locations on the green genome, we used the mlod scores >5 between markers to confirm the robustness of markers for each lg. the highmap strategy was utilized to order the slaf markers and correct genotyping errors within lgs, in order to ensure the efficient construction of a high-density and high-quality map (liu d.y. et […]

PMCID: 5859152
PMID: 29555986
DOI: 10.1038/s41598-018-23173-0

[…] distortion (p < 0.01) resulted from a chi-square test were excluded. eventually, 5,380 snp markers were selected for genetic map construction.table 2, altogether, 5,380 snps were loaded into highmap software. through linkage analysis, 5,225 snps (97.21%) were anchored to the map, distributing over 11 linkage groups (lgs). information of these snp markers and their corresponding slaf […]

PMCID: 5937187
PMID: 29487138
DOI: 10.1534/genetics.117.300627

[…] outcrossed full-sibling (full-sib) families. recently, two software packages have been developed for performing linkage mapping in full-sib families using sequencing data. these are lep-map (, ) and highmap (), both of which address the computational problem associated with high-density maps but are not specifically designed to handle low coverage sequencing data., another complication […]

PMCID: 5776132
PMID: 29387076
DOI: 10.3389/fpls.2017.02269

[…] fragments (slafs) were processed to obtain the slaf genotype of each sample (sun et al., )., a total of 5,472 polymorphic slafs was obtained from the rad-seq data of dj15 and koshihikari. using highmap method as described by liu et al. (), a high density linkage map was constructed from the slaf genotyping data of 103 f2:4 lines. next, qtl were identified by the composite interval mapping […]


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HighMap institution(s)
Biomarker Technologies Corporation, Beijing, China; Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; State Key laboratory of Crop Genetic and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
HighMap funding source(s)
This work was supported by a National Program on Key Basic Research Projects (the 973 Program: 2012CB113906 and 2012CB113900), a National High Technology Research and Development Program of China (the 863 Program, No. 2012AA100101).

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