Alternatives and similar repositories for HaploSweep

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

• WarrenLab / chicken-pangenome-paper
  Scripts used to perform analyses in Rice et al. (2023)
  ☆15Updated last year
• jydu / maffilter
  The MafFilter genome alignment processor
  ☆19Updated 3 months ago
• DessimozLab / OMAnnotator
  Consensus genome annotation using OMA
  ☆26Updated 2 months ago
• noecochetel / North_American_Vitis_Pangenome
  Construct and Analyze the North American Vitis pangenome
  ☆24Updated last week
• LeilyR / Multi-genome-Reference
  A program to generate a graph which presents a simplified representation of several full length genomes
  ☆13Updated 7 years ago
• idanefroni / Conservatory
  Identification of conserved non-coding sequences in plants
  ☆21Updated 3 months ago
• dfguan / pin_hic
  A Hi-C scaffolding method
  ☆22Updated 3 years ago
• andreaminio / HaploSync
  Tools for haplotype-wise reconstruction of pseudomolecules
  ☆20Updated 10 months ago
• Sendrowski / fastDFE
  Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annot…
  ☆17Updated 3 weeks ago
• avaughn271 / CLUES2
  The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.
  ☆15Updated 4 months ago
• ChenHuaLab / Beta-PSMC
  ☆12Updated 5 years ago
• davidebolo1993 / cosigt
  ☆20Updated last week
• Markusjsommer / TD2
  TD2
  ☆15Updated 2 months ago
• ChenHuaLab / CEGA
  Inferring natural selection by comparative population genomic analysis across species
  ☆24Updated last year
• yangli557 / AnnoSINE
  SINE annotation tool for plant genomes
  ☆18Updated last year
• alshai / vcf2msa
  convert a multi-sample VCF file to a multiple sequence alignment (C)
  ☆14Updated 6 years ago
• njdbickhart / GoatAssemblyScripts
  A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
  ☆11Updated 8 years ago
• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆31Updated 4 years ago
• Uauy-Lab / pangenome-haplotypes
  Scripts to do haplotype analysis on pan genomes.
  ☆21Updated 4 years ago
• shingocat / syntenyPlotByR
  plot genome alignment synteny
  ☆21Updated 5 years ago
• kammoji / gapFinisher
  A reliable gap filling pipeline for draft genomes
  ☆11Updated 5 years ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 2 months ago
• schneebergerlab / GameteBinning
  ☆12Updated 4 years ago
• ksiewert / BetaScan
  Genome-wide scan for balancing selection using beta statistic
  ☆29Updated 2 years ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆20Updated 8 months ago
• zstephens / telogator
  A method for measuring chromosome-specific telomere length from long reads
  ☆22Updated last year
• glogsdon1 / sunk-based_assembly
  ☆15Updated 4 years ago
• schneebergerlab / GameteBinning_tetraploid
  This is used to achieve haplotype-resolved assembly of tetraploid genomes using gamete sequencings
  ☆12Updated 3 years ago
• evotools / CattleGraphGenomePaper
  Set of script for the paper on the cattle graph genome
  ☆13Updated 2 years ago