Alternatives and similar repositories for pgr-tk:

Users that are interested in pgr-tk are comparing it to the libraries listed below

• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆93Updated this week
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆111Updated last month
• PacificBiosciences / HiPhase
  Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
  ☆72Updated 4 months ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆109Updated 2 months ago
• TimD1 / vcfdist
  vcfdist: Accurately benchmarking phased variant calls
  ☆79Updated this week
• daewoooo / SVbyEye
  ☆75Updated 4 months ago
• lh3 / dipcall
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆99Updated 3 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆100Updated 2 weeks ago
• KolmogorovLab / hapdup
  Pipeline to convert a haploid assembly into diploid
  ☆96Updated 3 weeks ago
• colindaven / awesome-pangenomes
  A list of software for pangenomics
  ☆98Updated this week
• PacificBiosciences / pb-human-wgs-workflow-snakemake
  DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
  ☆38Updated last year
• kjenike / panagram
  ☆61Updated last week
• DecodeGenetics / Ratatosk
  Hybrid error correction of long reads using colored de Bruijn graphs
  ☆100Updated 4 months ago
• lh3 / srf
  SRF: Satellite Repeat Finder
  ☆90Updated last year
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆114Updated last week
• mobinasri / flagger
  Evaluating genome assemblies
  ☆83Updated last week
• nhansen / SVanalyzer
  Tools for the analysis of structural variation in genomes
  ☆78Updated 10 months ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆86Updated 10 months ago
• nanoporegenomics / napu_wf
  WDL workflows for variant calling and assembly using ONT
  ☆32Updated 2 weeks ago
• fritzsedlazeck / Spectre
  Copy number caller for long read data including SNV utilization
  ☆55Updated 4 months ago
• arangrhie / merfin
  Evaluate variant calls and its combination with k-mer multiplicity
  ☆65Updated 2 years ago
• sheinasim-USDA / HiFiAdapterFilt
  Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
  ☆85Updated 6 months ago
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆112Updated 4 months ago
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆45Updated 4 years ago
• TF-Chan-Lab / panGraphViewer
  Show pangenome graphs in an easy way
  ☆54Updated 2 years ago
• PacificBiosciences / HiFiCNV
  Copy number variant caller and depth visualization utility for PacBio HiFi reads
  ☆40Updated 3 months ago
• shilpagarg / WHdenovo
  ☆47Updated 4 years ago
• Kuanhao-Chao / LiftOn
  🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies
  ☆71Updated 2 months ago
• 0xTCG / biser
  A fast tool for detecting and decomposing segmental duplications in genome assemblies
  ☆46Updated last year
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆50Updated 2 years ago