Alternatives and similar repositories for gaffer:

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

• chfi / gfainject
  ☆15Updated last year
• rchikhi / 2022-pangenome-graphs-intro
  ☆21Updated 4 months ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆22Updated 3 weeks ago
• dubssieg / pancat
  Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
  ☆33Updated 3 weeks ago
• thegenemyers / PHASE-MERS
  Utilities to detect and profile `het-kmers`
  ☆11Updated 6 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆23Updated 3 weeks ago
• lh3 / gffio
  ☆32Updated 2 years ago
• pangenome / pgge
  the pangenome graph evaluator
  ☆24Updated 3 years ago
• marschall-lab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated this week
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated last year
• ryought / mummer-idotplot
  Generate interactive dotplot from mummer4 output using plotly
  ☆26Updated 4 years ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• tprodanov / locityper
  Targeted genotyper for complex polymorphic genes
  ☆19Updated last week
• PacificBiosciences / actc
  Align subreads to ccs reads
  ☆13Updated last year
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆26Updated 5 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 3 months ago
• MoinSebi / gSV
  ☆11Updated 2 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated 9 months ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 5 months ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆21Updated 6 months ago
• pierrepeterlongo / back_to_sequences
  ☆41Updated 3 months ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• thegenemyers / MERQURY.FK
  FastK based version of Merqury
  ☆22Updated last week
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 3 months ago
• T2T-apes / ape_pangenome
  pangenome analyses for complete genomes of great apes (and gibbon)
  ☆17Updated 4 months ago
• ComparativeGenomicsToolkit / taffy
  This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
  ☆25Updated 2 months ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆17Updated 2 months ago