Alternatives and similar repositories for pgvf-spec

Users that are interested in pgvf-spec are comparing it to the libraries listed below

• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆26Updated 3 weeks ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated last year
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆40Updated 2 years ago
• pangenome / pgge
  the pangenome graph evaluator
  ☆29Updated 4 years ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 3 years ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆23Updated last year
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated last month
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆29Updated last year
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 7 months ago
• GTPB / CPANG22
  Computational Pangenomics
  ☆17Updated 3 years ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆34Updated 5 years ago
• AndreaGuarracino / paf2chain
  convert PAF format to CHAIN format
  ☆34Updated 7 months ago
• zeeev / DASVC
  De-novo Assembly Structural Variant Caller
  ☆13Updated 9 years ago
• at-cg / RAFT
  ☆30Updated last year
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆28Updated last year
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated last year
• marbl / training
  Genome Assembly 102
  ☆17Updated 8 months ago
• PacificBiosciences / portello
  Transfer HiFi read mappings from their own assembly contigs to a standard reference
  ☆27Updated last week
• rchikhi / 2022-pangenome-graphs-intro
  ☆28Updated last year
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆15Updated 4 months ago
• jydu / maffilter
  The MafFilter genome alignment processor
  ☆19Updated last week
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆31Updated 6 months ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆20Updated last year
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆21Updated last year
• MoinSebi / gfa2bin
  ☆28Updated 4 months ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago