ngsRelateV2

"ngsRelateV2" represents a significant update to the original ngsRelate tool, specifically designed to estimate relatedness from high-throughput sequencing (HTS) data. This advanced version accurately determines relatedness among individuals, including those who may be inbred, by calculating the nine condensed Jacquard coefficients and other relatedness statistics.

Key Features and Functionalities:

- Enhanced Inbred Individuals Analysis: Unlike its predecessor, ngsRelateV2 incorporates the analysis of inbred individuals, offering a more comprehensive understanding of genetic relatedness.

- Efficient Performance: The program is optimized for performance with threading capabilities, ensuring it scales linearly with the number of cores allocated, enhancing its efficiency for large datasets.

- Compatibility with Common Data Formats: ngsRelateV2 can directly work with commonly used data formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF), eliminating data conversion.

Topic

Genotype and phenotype;Sequencing;Population genetics

Detail

  • Operation: Parsing;Genotyping;Protein threading

  • Software interface: Command-line interface

  • Language: C++,C

  • License: The GNU General Public License v3.0

  • Cost: Free with restrictions

  • Version name: -

  • Credit: Danish National Research Foundation, Initiative d’Excellence Chaires d’attractivité, Université de Toulouse, Carlsberg Foundation, Lundbeck Foundation, Independent Research Fund Denmark, ERC.

  • Input: BAM, CRAM, VCF, BCF

  • Output: -

  • Contact: Kristian Hanghøj k.hanghoej@snm.ku.dk ,Thorfinn Sand Korneliussen tskorneliussen@snm.ku.dk ,Ida Moltke ida@binf.ku.dk

  • Collection: -

  • Maturity: Mature

Publications

  • Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.
  • Hanghøj K, et al. Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding. Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding. 2019; 8:(unknown pages). doi: 10.1093/gigascience/giz034
  • https://doi.org/10.1093/GIGASCIENCE/GIZ034
  • PMID: 31042285
  • PMC: PMC6488770

Download and documentation

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