Alternatives and similar repositories for hapdup

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

• codialab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆116Updated 2 weeks ago
• nanoporetech / duplex-tools
  Splitting of sequence reads by internal adapter sequence search
  ☆51Updated 2 years ago
• PacificBiosciences / jasmine
  Call select base modifications in PacBio HiFi reads
  ☆15Updated last month
• daewoooo / SVbyEye
  ☆144Updated last month
• lh3 / srf
  SRF: Satellite Repeat Finder
  ☆101Updated last year
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆102Updated 5 months ago
• eldariont / svim-asm
  Structural Variant Identification Method using Genome Assemblies
  ☆129Updated 3 years ago
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆49Updated last month
• colindaven / awesome-pangenomes
  A list of software for pangenomics
  ☆165Updated 2 weeks ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆59Updated 2 years ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆130Updated last year
• mahulchak / svmu
  A program to call variants from genome alignment
  ☆81Updated 8 months ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆95Updated 8 months ago
• lh3 / dipcall
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆105Updated 4 years ago
• kjenike / panagram
  ☆68Updated last week
• LiLabAtVT / DeepTE
  Neural network classification of TE
  ☆97Updated 2 months ago
• mapleforest / HaploMerger2
  ☆45Updated 9 years ago
• SAMtoBAM / MUMandCo
  MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
  ☆75Updated 3 months ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆76Updated 4 years ago
• Kuanhao-Chao / LiftOn
  🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies
  ☆116Updated last month
• AntonBankevich / LJA
  ☆119Updated 2 months ago
• twolinin / longphase
  ☆121Updated last month
• KamilSJaron / k-mer-approaches-for-biodiversity-genomics
  k-mer learning materials
  ☆81Updated 10 months ago
• yangao07 / longcallD
  A local-haplotagging-based small and structural variant caller
  ☆90Updated last week
• paoloshasta / shasta
  De novo assembly from Oxford Nanopore reads.
  ☆88Updated last month
• yeeus / GCI
  A program for assessing the T2T genome continuity
  ☆92Updated 2 weeks ago
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆81Updated last year
• 4ureliek / Parsing-RepeatMasker-Outputs
  Few scripts facilitating the extraction of info from Repeat Masker .out files
  ☆84Updated 4 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆54Updated last year
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆120Updated 2 months ago