Alternatives and similar repositories for gaftools

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

• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated last year
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated 2 years ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated last year
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 4 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆26Updated this week
• tlemane / kmdiff
  Differential k-mer analysis
  ☆37Updated last year
• tprodanov / locityper
  Targeted genotyper for complex polymorphic genes
  ☆28Updated last week
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated 10 months ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 3 years ago
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆27Updated last year
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆32Updated 4 years ago
• human-pangenomics / hprc-tutorials
  ☆18Updated last year
• rchikhi / 2022-pangenome-graphs-intro
  ☆28Updated last year
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆25Updated 11 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 6 months ago
• MoinSebi / gfa2bin
  ☆25Updated 2 months ago
• pangenome / pgge
  the pangenome graph evaluator
  ☆29Updated 4 years ago
• cumtr / PG-SCUnK
  PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers
  ☆19Updated last month
• asylvz / SVarp
  Phased structural variant discovery in pangenomes
  ☆37Updated last year
• davidebolo1993 / cosigt
  COsine-based SImilarity Genotyper using pangenomes
  ☆21Updated this week
• pierrepeterlongo / back_to_sequences
  ☆45Updated last week
• fawaz-dabbaghieh / bubble_gun
  ☆40Updated 2 months ago
• ablab / stringdecomposer
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆35Updated 3 years ago
• at-cg / RAFT
  ☆28Updated last year
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆16Updated last year
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆50Updated 2 years ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆35Updated 4 months ago
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago