Alternatives and similar repositories for pangenome-haplotypes

Users that are interested in pangenome-haplotypes are comparing it to the libraries listed below

• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• yangli557 / AnnoSINE
  SINE annotation tool for plant genomes
  ☆18Updated last year
• schneebergerlab / GameteBinning_tetraploid
  This is used to achieve haplotype-resolved assembly of tetraploid genomes using gamete sequencings
  ☆12Updated 4 years ago
• dawelab / Ab10-Assembly
  B73Ab10 genome assembly methods
  ☆16Updated 3 years ago
• dfguan / pin_hic
  A Hi-C scaffolding method
  ☆22Updated 4 years ago
• shingocat / syntenyPlotByR
  plot genome alignment synteny
  ☆21Updated 5 years ago
• YaoZhou89 / WGSc
  ☆15Updated 4 years ago
• phasegenomics / matlock
  Simple tools for working with Hi-C data
  ☆18Updated 7 years ago
• weigelworld / pan-nlrome
  The GitHub repository for the A. thaliana pan-NLR'ome project.
  ☆18Updated 6 years ago
• oushujun / PopTEvo
  Study of TE evolution in a population of genomes
  ☆10Updated 2 years ago
• mcsimenc / PhyLTR
  Phylogenetic Analysis of Long Terminal Repeat Retrotransposons
  ☆18Updated 3 years ago
• SamueleSoraggi / HMMploidy
  A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models
  ☆18Updated 3 years ago
• noecochetel / North_American_Vitis_Pangenome
  Construct and Analyze the North American Vitis pangenome
  ☆29Updated 5 months ago
• esolares / HapSolo
  Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding
  ☆20Updated 10 months ago
• sanger-tol / yahs
  Yet another Hi-C scaffolding tool
  ☆22Updated last year
• andreaminio / HaploSync
  Tools for haplotype-wise reconstruction of pseudomolecules
  ☆22Updated 4 months ago
• maiziezhoulab / LRSV_combo
  Long Read Based SV Calling Tools Analysis
  ☆14Updated last year
• glogsdon1 / sunk-based_assembly
  ☆16Updated 4 years ago
• vgteam / sv-genotyping-paper
  ☆31Updated 6 years ago
• DessimozLab / OMAnnotator
  Consensus genome annotation using OMA
  ☆31Updated this week
• yilinZhang-bio / Watermelon-pangenome
  ☆27Updated 2 years ago
• caasivfbioinfo / Bol_pangenome
  ☆16Updated 2 years ago
• reubwn / collinearity
  scripts to parse and analyse MCScanX collinearity output
  ☆33Updated 5 years ago
• Wenfei-Xian / TIPP
  Telomere local assembly, Improved whole genome polish, and Plastid assembly
  ☆22Updated 8 months ago
• legumeinfo / pandagma
  Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.
  ☆20Updated 2 weeks ago
• yiliao1022 / LASTZ_SV_pipeline
  ☆16Updated 6 years ago
• LAILAB-CAU / update-Mo17
  ☆29Updated 2 years ago
• yiliao1022 / SVGAP
  A pipeline for genomic variant detection with genome assemblies at population scale
  ☆36Updated 7 months ago
• simonhmartin / asynt
  Genome alignment and synteny plots
  ☆33Updated 2 years ago
• schatzlab / pseudohaploid
  Create a pseudohaploid assembly from a partially resolved diploid assembly
  ☆32Updated 6 years ago