HAF-pipe

HAF-pipe is a software tool to efficiently estimate allele frequencies in evolve-and-resequence (E+R) experiments using low-coverage sequencing data. The key features and functionalities of the HAF-pipe are:

1. Haplotype inference: HAF-pipe infers known founder haplotypes in small genomic windows, enabling accurate estimation of allele frequencies even with shallow sequencing depths (<5x coverage).

2. Applicability to various organisms: The tool can be used to estimate frequencies for bi-allelic SNPs in populations of any model organism, as long as the populations are founded with sequenced homozygous strains.

3. Cost-effective: By leveraging low-coverage sequencing data, HAF-pipe reduces the cost associated with high-coverage sequencing (>100x) of multiple pooled samples, typically required for detecting adaptive alleles by comparing frequency trajectories from replicate populations.

Topic

DNA polymorphism;Sequencing;Population genetics;Genotype and phenotype

Detail

  • Operation: Imputation;SNP detection;Haplotype mapping;Genotyping

  • Software interface: Command-line user interface

  • Language: Shell,Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The National Science Foundation (NSF), the National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: Sharon Greenblum greensi@lbl.gov

  • Collection: -

  • Maturity: -

Publications

  • Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments.
  • Tilk S, et al. Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. 2019; 9:4159-4168. doi: 10.1534/g3.119.400755
  • https://doi.org/10.1534/G3.119.400755
  • PMID: 31636085
  • PMC: PMC6893198

Download and documentation

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