Alternatives and similar repositories for SpecHap

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

• PacificBiosciences / trgt-denovo
  De novo tandem repeat calling from PacBio HiFi data
  ☆18Updated 4 months ago
• AlgoLab / pantas
  Differential quantification of alternative splicing events on spliced pangenome graphs
  ☆14Updated 8 months ago
• rlorigro / simple-dotplot
  Very simple and configurable all-in-one dotplot program
  ☆14Updated 2 years ago
• sinamajidian / phaseme
  A tool set to assess the quality of the per read phasing and reduce the errors.
  ☆12Updated 5 years ago
• oscarlr / MsPAC
  Phase reads, assemble haplotypes and detect SVs
  ☆19Updated 4 years ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated last year
• esrice / trio_binning
  Programs implementing the trio-binning genome assembly method
  ☆18Updated last year
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆32Updated 4 years ago
• zhixingfeng / iGDA
  Detect and phase minor SNVs from long-read sequencing data
  ☆14Updated 3 years ago
• ndierckx / combiSV
  Combine structural variation outputs from long sequencing reads into a superior call set
  ☆18Updated 2 months ago
• fritzsedlazeck / SVCollector
  Method to optimally select samples for validation and resequencing
  ☆28Updated 4 years ago
• hitbc / gcSV
  ☆21Updated 7 months ago
• ablab / stringdecomposer
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆35Updated 3 years ago
• jydu / maffilter
  The MafFilter genome alignment processor
  ☆19Updated 5 months ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated 10 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• KolmogorovLab / hapdiff
  SV calling for diploid assemblies
  ☆28Updated last year
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• micahvista / VACmap
  VACmap: a long-read aligner specifically designed for complex structural variation discovery
  ☆36Updated 2 months ago
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆25Updated 4 years ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆32Updated this week
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated last month
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• tobiasrausch / lorax
  A long-read analysis toolbox for cancer and population genomics
  ☆23Updated 3 months ago
• Xinglab / TideHunter
  TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
  ☆21Updated last year
• TNTurnerLab / HAT
  HAT is a set of tools for calling de novo variants from whole-genome sequencing data.
  ☆24Updated last year
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated last year
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆16Updated last year
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• bcgsc / goldrush
  Linear-time de novo Long Read Assembler
  ☆41Updated 8 months ago