Alternatives and similar repositories for VGpop

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

• pangenome / pgvf-spec
  Pangenome Graph Variation Format (PGVF)
  ☆20Updated 4 years ago
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆33Updated 4 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
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated 2 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆24Updated 2 months ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆26Updated last year
• MoinSebi / gfa2bin
  ☆25Updated 3 weeks ago
• jts / mbtools
  ☆14Updated last year
• ekg / gimbricate
  recompute GFA link overlaps
  ☆26Updated 2 years ago
• hanzou666 / msa2gfa
  A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg
  ☆12Updated 6 years ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated 2 weeks ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated last year
• huangnengCSU / BlockPolish
  BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
  ☆17Updated 2 years ago
• Gaius-Augustus / clamsa
  ClaMSA (Classify Multiple Sequence Alignments).
  ☆13Updated 9 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated 9 months ago
• fawaz-dabbaghieh / bubble_gun
  ☆42Updated 3 weeks ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• pangenome / gfagino
  your friendly pangenome graph genotyper
  ☆10Updated 2 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 10 months ago
• edawson / svaha
  Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
  ☆12Updated last year
• chfi / gfainject
  ☆17Updated 2 years ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 3 weeks ago
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆23Updated 2 months ago
• langmead-lab / vargas
  ☆25Updated this week
• VGP / vgp-tools
  ☆28Updated 4 months ago
• atifrahman / SWALO
  Scaffolding with assembly likelihood optimization
  ☆22Updated 4 years ago
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆21Updated 5 months ago