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UGbS-Flex

UGbS-Flex

UGbS-Flex consists of a set of script to combine publicly available software tools for single nucleotide polymorphism (SNP) detection - genotyping by sequencing. The UGbS-Flex pipeline can use paired-end reads as an input.

Topic

DNA polymorphism; Genetics; Genetic variation

Details

  • Operation: Genotyping; Mapping; Genetic variation analysis; SNP detection
  • Software interface: Command-line user interface
  • Language: Python, Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: BioInnovate Africa Program, University of Georgia, ulbright-Nehru Senior Research Fellowship,the United States India Educational Foundation, New Delhi, Indi, Department of Energy (DOE)
  • Contact: Peng Qi pengqi _at_ uga.edu
  • Collection: -

Publications

Qi P, Gimode D, Saha D, Schroder S, Chakraborty D, Wang X, Dida MM, Malmberg RL, Devos KM "UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study." BMC Plant Biol. 2018 Jun 15;18(1):117. https://doi.org/10.1186/s12870-018-1316-3
PMID: 29902967
PMCID: PMC6003085


Download and documentation




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