Alternatives and similar repositories for pgvf-spec:

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

• hanzou666 / msa2gfa
  A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg
  ☆12Updated 6 years ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 5 months ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 7 months ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• jmonlong / pangenome-evaluation
  Pipeline to evaluate pangenomes, e.g. from the variation it contains or how well reads map
  ☆10Updated 3 years ago
• pangenome / pgge
  the pangenome graph evaluator
  ☆26Updated 4 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated 11 months ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• Flavia95 / VGpop
  Population genetics analysis on VG
  ☆17Updated 3 years ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆36Updated last year
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆33Updated 4 years ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆23Updated 2 months ago
• T2T-apes / ape_pangenome
  pangenome analyses for complete genomes of great apes (and gibbon)
  ☆17Updated 6 months ago
• Adamtaranto / blast-besties
  Rapid discovery of reciprocal best blast pairs.
  ☆10Updated 5 months ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆24Updated this week
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated 10 months ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 9 months ago
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 3 years ago
• bcgsc / ntLink
  Minimizer-based assembly scaffolding and mapping using long reads
  ☆38Updated 6 months ago
• MoinSebi / gfa2bin
  ☆19Updated 4 months ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆17Updated 4 months ago
• chfi / gfainject
  ☆15Updated last year
• lh3 / gffio
  ☆32Updated 2 years ago
• jts / mbtools
  ☆14Updated last year
• marbl / training
  Genome Assembly 102
  ☆14Updated 3 months ago
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated 9 months ago
• MoinSebi / gSV
  ☆11Updated 2 years ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated 8 months ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 5 months ago