Alternatives and similar repositories for pangenie:

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

• EichlerLab / pav
  Phased assembly variant caller
  ☆112Updated 4 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆114Updated this week
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆80Updated 2 months ago
• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆100Updated last month
• colindaven / awesome-pangenomes
  A list of software for pangenomics
  ☆110Updated last week
• twolinin / longphase
  ☆110Updated last month
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆126Updated last week
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆112Updated 3 weeks ago
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆113Updated last week
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆76Updated 10 months ago
• KolmogorovLab / hapdup
  Pipeline to convert a haploid assembly into diploid
  ☆100Updated 2 months ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆142Updated last month
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆125Updated 8 months ago
• CSU-KangHu / HiTE
  High-precision TE Annotator
  ☆109Updated this week
• marbl / ModDotPlot
  ☆143Updated this week
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆186Updated 2 weeks ago
• xjtu-omics / SVision
  Detecting genome structural variants with deep learning in single molecule sequencing
  ☆107Updated last week
• eldariont / svim
  Structural Variant Identification Method using Long Reads
  ☆170Updated 3 years ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆110Updated 9 months ago
• xiaochuanle / MECAT2
  ☆71Updated 4 years ago
• eldariont / svim-asm
  Structural Variant Identification Method using Genome Assemblies
  ☆108Updated 2 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• wdecoster / cramino
  A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
  ☆145Updated 2 weeks ago
• daewoooo / SVbyEye
  ☆86Updated last month
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆97Updated last year
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆97Updated last year
• aaranyue / quarTeT
  A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
  ☆130Updated last month
• starskyzheng / panpop
  Application of pan-genome for population
  ☆104Updated 6 months ago
• marbl / HG002
  A complete diploid human genome
  ☆117Updated 3 months ago
• lh3 / dipcall
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆100Updated 3 years ago