V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data | Article Information | J-GLOBAL (2025)

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J-GLOBAL ID:202302242365877683Reference number:23A2927652

V-primer:マルチサンプルバリアントコールフォーマット(VCF)遺伝子タイピングデータからゲノム全体のInDelおよびSNPマーカーを効率的に設計するためのソフトウェア

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Author(9):

Natsume Satoshi

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

Nomura Chihiro

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

Utsushi Hiroe

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

Shimizu Motoki

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

Terauchi Ryohei

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center

,

Terauchi Ryohei

(Crop Evolution Laboratory, Kyoto University)

About Crop Evolution Laboratory, Kyoto University

,

(Department of Genomics and Breeding, Iwate Biotechnology Research Center)

About Department of Genomics and Breeding, Iwate Biotechnology Research Center


Material:

Breeding Science(Breed Sci)

About Breeding Science


Volume:

73Issue:

4Page:

415-420(J-STAGE)Publication year:

2023
JST Material Number:

Y0311BISSN:

1344-7610Document type:

Article
Article type:

短報Country of issue:

Japan (JPN)Language:

ENGLISH (EN)

Thesaurus term:

Thesaurus term/Semi thesaurus term

Keywords indexed to the article.
All keywords is available on JDreamIII(charged).
On J-GLOBAL, this item will be available after more than half a year after the record posted. In addtion, medical articles require to login to MyJ-GLOBAL.

*software

About software

,...

Semi thesaurus term:

Thesaurus term/Semi thesaurus term

Keywords indexed to the article.
All keywords is available on JDreamIII(charged).
On J-GLOBAL, this item will be available after more than half a year after the record posted. In addtion, medical articles require to login to MyJ-GLOBAL.

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Author keywords(7):

molecular marker

About molecular marker

,

primer design

About primer design

,

,

,

next-generation sequencing

About next-generation sequencing

,

genomics

About genomics

,

breeding

About breeding

JST classification(2):

JST classification
Category name(code) classified by JST.

Plant breeding in general

(FC02010K)

About Plant breeding in general

,Research methods in genetics

(EC01020N)

About Research methods in genetics

Reference(19):

  • Baird, N.A., P.D. Etter, T.S. Atwood, M.C. Currey, A.L. Shiver, Z.A. Lewis, E.U. Selker, W.A. Cresko and E.A. Johnson (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376.
  • Bolger, A.M., M. Lohse and B. Usadel (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
  • Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer and T.L. Madden (2009) BLAST+: Architecture and applications. BMC Bioinformatics 10: 421.
  • Cock, P.J.A., T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski et al. (2009) Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
  • Danecek, P., A. Auton, G. Abecasis, C.A. Albers, E. Banks, M.A. DePristo, R.E. Handsaker, G. Lunter, G.T. Marth, S.T. Sherry et al. (2011) The variant call format and VCFtools. Bioinformatics 27: 2156-2158.

more...

Terms in the title(5):

Terms in the title
Keywords automatically extracted from the title.

遺伝子タイピング

About 遺伝子タイピング

,

ゲノム

About ゲノム

,

SNPマーカー

About SNPマーカー

,

設計

About 設計

,

ソフトウェア

About ソフトウェア


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V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data | Article Information | J-GLOBAL (2025)
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