Alternatives and similar repositories for LDhot

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

• ListerLab / TEPID
  Transposable element polymorphism identification
  ☆34Updated 5 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• MeHelmy / princess
  ☆83Updated 8 months ago
• Rosemeis / HaploNet
  Haplotype and population structure inference using neural networks.
  ☆27Updated 11 months ago
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆52Updated 4 years ago
• lstevison / vcf-conversion-tools
  Tools to convert to and from vcf format
  ☆14Updated 8 years ago
• ywchoi / phasing
  Evaluation of phasing performance
  ☆23Updated 7 years ago
• tpook92 / HaploBlocker
  R-package: Calculation of haplotype blocks and libraries
  ☆34Updated 4 months ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆50Updated 6 years ago
• stschiff / msmc2
  ☆65Updated 2 years ago
• EichlerLab / smrtsv2
  Structural variant caller
  ☆55Updated 3 years ago
• mrvollger / SDA
  Segmental Duplication Assembler (SDA).
  ☆44Updated 2 years ago
• auton1 / LDhat
  Estimate recombination rates from population genetic data
  ☆69Updated 5 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆38Updated 9 years ago
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆58Updated 2 months ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆49Updated 3 years ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆55Updated last year
• benedictpaten / marginPhase
  ☆35Updated 5 years ago
• fgvieira / ngsLD
  Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
  ☆47Updated 2 years ago
• mattravenhall / SV-Pop
  Upscaling SV detection to a multi-population level.
  ☆22Updated 4 months ago
• mklarqvist / tomahawk
  Fast calculations of linkage-disequilibrium in large-scale human cohorts
  ☆44Updated 6 years ago
• Rosemeis / pcangsd
  Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
  ☆56Updated 5 months ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 3 weeks ago
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• evotools / hapbin
  Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
  ☆45Updated 6 years ago
• bergmanlab / TELR
  TELR is a fast non-reference transposable element detector from long read sequencing data.
  ☆35Updated 2 years ago
• EichlerLab / pacbio_variant_caller
  SMRT-SV: Structural variant and indel caller for PacBio reads
  ☆28Updated 6 years ago
• vibansal / hapcut
  program for haplotype phasing from sequence reads and related tools
  ☆25Updated 7 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆39Updated last year
• stschiff / msmc-tools
  Tools and Utilities for msmc and msmc2
  ☆49Updated 3 months ago