Alternatives and similar repositories for pgge:

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

• GTPB / CPANG22
  Computational Pangenomics
  ☆17Updated 2 years ago
• mrvollger / NucFreq
  ☆35Updated last year
• marschall-lab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated last week
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 9 months ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated 6 months ago
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated last year
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 4 months ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆37Updated 5 months ago
• MoinSebi / gretl
  Statistics and analysis for variation graphs
  ☆38Updated 3 months ago
• thegenemyers / MERQURY.FK
  FastK based version of Merqury
  ☆22Updated last week
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆23Updated last month
• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆30Updated 3 years ago
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆26Updated 3 years ago
• vgteam / sv-genotyping-paper
  ☆30Updated 5 years ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated 3 weeks ago
• pangenome / HPRCyear1v2genbank
  building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
  ☆14Updated 2 years ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated 7 months ago
• ablab / TandemTools
  Tool for assessing/improving assembly quality in extra-long tandem repeats
  ☆46Updated 4 years ago
• davidebolo1993 / cosigt
  ☆15Updated last week
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆28Updated 3 months ago
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 3 years ago
• baoxingsong / genomeAlignment
  Compare different genome alignment tools using a wide range of genomes with different complexities.
  ☆13Updated 2 years ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• ablab / stringdecomposer
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆36Updated 2 years ago
• lipingfangs / VAP
  a programme for visualization of short sequence alignment and path navigation in graphical pan-genome
  ☆23Updated last year
• at-cg / RAFT
  ☆22Updated 7 months ago
• KolmogorovLab / hapdiff
  SV calling for diploid assemblies
  ☆26Updated last year
• marbl / rukki
  Extracting paths from assembly graphs
  ☆22Updated 10 months ago
• schatzlab / pseudohaploid
  Create a pseudohaploid assembly from a partially resolved diploid assembly
  ☆32Updated 5 years ago