Alternatives and similar repositories for HapHiC:

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

• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆185Updated 2 weeks ago
• c-zhou / yahs
  Yet another Hi-C scaffolding tool
  ☆146Updated 6 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆200Updated last year
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆222Updated 3 months ago
• aaranyue / quarTeT
  A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
  ☆130Updated last month
• SunPengChuan / wgdi
  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
  ☆135Updated 4 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆176Updated 6 months ago
• TobyBaril / EarlGrey
  Earl Grey: A fully automated TE curation and annotation pipeline
  ☆168Updated last week
• jtlovell / GENESPACE
  ☆206Updated 3 months ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆254Updated 4 months ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆181Updated 2 months ago
• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆209Updated this week
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆202Updated last month
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆151Updated 3 years ago
• HuiyangYu / PanDepth
  An ultra-fast and efficient genomic tool for coverage calculation
  ☆147Updated last month
• PASApipeline / PASApipeline
  PASA software
  ☆188Updated 2 months ago
• chenlianfu / geta
  ☆78Updated 9 months ago
• baoxingsong / AnchorWave
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆168Updated 6 months ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆171Updated 4 months ago
• ruanjue / smartdenovo
  Ultra-fast de novo assembler using long noisy reads
  ☆135Updated 4 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated 11 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆210Updated last year
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆276Updated 3 weeks ago
• hahnlab / CAFE5
  Version 5 of the CAFE phylogenetics software
  ☆131Updated 2 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• wdecoster / chopper
  ☆185Updated last week
• BGI-shenzhen / VCF2Dis
  VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Forma…
  ☆91Updated last month
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆205Updated 2 years ago
• dfguan / purge_dups
  haplotypic duplication identification tool
  ☆238Updated last year
• ncbi / egapx
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
  ☆133Updated last month