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
  ☆26Updated 3 months ago
• rchikhi / 2022-pangenome-graphs-intro
  ☆21Updated 3 months ago
• marschall-lab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆35Updated last week
• lh3 / gffio
  ☆32Updated 2 years ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated last month
• fawaz-dabbaghieh / bubble_gun
  ☆40Updated 2 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆22Updated last month
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated last year
• pangenome / pgge
  the pangenome graph evaluator
  ☆24Updated 3 years ago
• ComparativeGenomicsToolkit / taffy
  This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
  ☆24Updated last month
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆21Updated 5 months ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆30Updated 3 years ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆36Updated last year
• human-pangenomics / hprc-tutorials
  ☆14Updated 9 months ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆21Updated 10 months ago
• dubssieg / pancat
  Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
  ☆32Updated last month
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 6 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated last month
• asylvz / SVarp
  Phased structural variant discovery in pangenomes
  ☆30Updated 7 months ago
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆26Updated 3 years ago
• mktle / colorSV
  somatic SV calling on matched tumor-normal co-assembly graphs
  ☆18Updated 5 months ago
• pierrepeterlongo / back_to_sequences
  ☆41Updated last month
• vpc-ccg / sedef
  Identification of segmental duplications in the genome
  ☆26Updated 2 years ago
• pangenome / HPRCyear1v2genbank
  building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
  ☆14Updated last year
• esrice / trio_binning
  Programs implementing the trio-binning genome assembly method
  ☆19Updated last year
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆33Updated 4 years ago
• tprodanov / locityper
  Targeted genotyper for complex polymorphic genes
  ☆13Updated 3 weeks ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated 7 months ago