Alternatives and similar repositories for ngsLD

Users that are interested in ngsLD are comparing it to the libraries listed below

• PhHermann / LDJump
  R Package to Estimate Variable Recombination Rates using Population Genetic Data
  ☆43Updated 6 years ago
• Rosemeis / pcangsd
  Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
  ☆56Updated 5 months ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆76Updated 4 years ago
• auton1 / LDhat
  Estimate recombination rates from population genetic data
  ☆70Updated 5 years ago
• MikkelSchubert / paleomix
  Pipelines and tools for the processing of ancient and modern HTS data.
  ☆47Updated last month
• petrelharp / local_pca
  Methods for examining PCA locally along the genome.
  ☆86Updated last year
• popgenmethods / momi2
  Infer demographic history with the Moran model
  ☆50Updated 5 months ago
• clwgg / nQuire
  A statistical framework for ploidy estimation using NGS short-read data
  ☆62Updated 7 years ago
• stschiff / msmc-tools
  Tools and Utilities for msmc and msmc2
  ☆49Updated 4 months ago
• stschiff / msmc2
  ☆65Updated 3 years ago
• stevemussmann / admixturePipeline
  A pipeline that accepts a VCF file to run through Admixture
  ☆63Updated 11 months ago
• ngarud / SelectionHapStats
  SelectionHapStats is a repository of Python scripts written to identify natural selection events in the genome and R scripts written to v…
  ☆27Updated 7 years ago
• mfumagalli / ngsPopGen
  Population genetics analyses from NGS data
  ☆25Updated 4 years ago
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 6 years ago
• paula-tataru / polyDFE
  predicting DFE and alpha from polymorphism data
  ☆28Updated 7 years ago
• tsackton / linked-selection
  ☆24Updated 8 years ago
• joepickrell / pophistory-tutorial
  Tutorial on using popular tools for learning about population history
  ☆52Updated 7 years ago
• schneebergerlab / findGSE
  findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a ske…
  ☆38Updated last year
• pkalbers / geva
  Genealogical Estimation of Variant Age (GEVA)
  ☆31Updated 4 years ago
• russcd / Ancestry_HMM
  ☆31Updated 2 years ago
• arangrhie / merfin
  Evaluate variant calls and its combination with k-mer multiplicity
  ☆67Updated 3 years ago
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆71Updated 2 months ago
• rwdavies / QUILT
  QUILT: Low coverage whole genome sequence imputation with large reference panels
  ☆65Updated last month
• evotools / hapbin
  Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
  ☆45Updated 6 years ago
• popgenmethods / SINGER
  Sampling and inference of genealogies with recombination
  ☆46Updated 5 months ago
• NBISweden / pipelines-nextflow
  A set of workflows written in Nextflow for Genome Annotation.
  ☆46Updated last year
• ANGSD / NgsRelate
  ☆44Updated 8 months ago
• alek0991 / iSAFE
  Pinpoints the mutation favored by selection
  ☆34Updated 4 years ago
• lh3 / unimap
  A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
  ☆87Updated 4 years ago
• josephryan / estimate_genome_size.pl
  Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
  ☆57Updated 2 years ago