Alternatives and similar repositories for mapquik

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

• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆45Updated last month
• PacificBiosciences / sawfish
  Joint structural variant and copy number variant caller for HiFi sequencing data
  ☆61Updated 2 weeks ago
• oma219 / spumoni
  Pan-Genomic Matching Statistics
  ☆53Updated last year
• UCSC-nanopore-cgl / MarginPolish
  MarginPolish: Graph based assembly polishing
  ☆46Updated 4 years ago
• lh3 / longdust
  Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
  ☆74Updated 3 weeks ago
• kjenike / panagram
  ☆66Updated last month
• seryrzu / unialigner
  ☆66Updated last year
• TF-Chan-Lab / panGraphViewer
  Show pangenome graphs in an easy way
  ☆56Updated 2 months ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆68Updated 3 months ago
• vikshiv / mumemto
  Mumemto: multi-MUM and MEM finding across pangenomes
  ☆113Updated last week
• yangao07 / longcallD
  A local-haplotagging-based small and structural variant caller
  ☆85Updated this week
• micahvista / VACmap
  VACmap: a long-read aligner specifically designed for complex structural variation discovery
  ☆36Updated 2 months ago
• kage-genotyper / kage
  Alignment-free genotyper for SNPs and short indels, implemented in Python.
  ☆52Updated 7 months ago
• lh3 / miniwfa
  A reimplementation of the WaveFront Alignment algorithm at low memory
  ☆49Updated last year
• univieCUBE / gepard
  Genome Pair Rapid Dotter
  ☆66Updated 4 years ago
• ablab / TandemTools
  Tool for assessing/improving assembly quality in extra-long tandem repeats
  ☆47Updated 4 years ago
• pangenome / impg
  implicit pangenome graph
  ☆71Updated last week
• mrvollger / SafFire
  ☆31Updated 5 months ago
• lh3 / calN50
  Compute N50/NG50 and auN/auNG
  ☆32Updated 2 years ago
• edawson / gfakluge
  A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
  ☆54Updated 3 years ago
• PacificBiosciences / MethBat
  A battery of methylation tools for PacBio HiFi reads
  ☆42Updated last month
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 4 months ago
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆51Updated 2 years ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 5 years ago
• pangenome / smoothxg
  linearize and simplify variation graphs using blocked partial order alignment
  ☆57Updated 2 months ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆92Updated 5 months ago
• ruanjue / bsalign
  Banded Striped DNA Sequence Alignment
  ☆47Updated 2 years ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆40Updated 11 months ago
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆49Updated 7 months ago
• Adamtaranto / teloclip
  A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
  ☆44Updated 6 months ago