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)
  ☆42Updated last week
• pangenome / impg
  implicit pangenome graph
  ☆58Updated this week
• kage-genotyper / kage
  Alignment-free genotyper for SNPs and short indels, implemented in Python.
  ☆49Updated 2 months ago
• UCSC-nanopore-cgl / MarginPolish
  MarginPolish: Graph based assembly polishing
  ☆46Updated 4 years ago
• oma219 / spumoni
  Pan-Genomic Matching Statistics
  ☆52Updated last year
• micahvista / VACmap
  VACmap: a long-read aligner specifically designed for complex structural variation discovery
  ☆35Updated 5 months ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆65Updated last month
• maickrau / ribotin
  ☆32Updated 2 weeks ago
• marschall-lab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated last month
• lh3 / calN50
  Compute N50/NG50 and auN/auNG
  ☆32Updated last year
• ablab / TandemTools
  Tool for assessing/improving assembly quality in extra-long tandem repeats
  ☆46Updated 4 years ago
• Adamtaranto / teloclip
  A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
  ☆36Updated 3 weeks ago
• kjenike / panagram
  ☆61Updated last month
• MoinSebi / gretl
  Statistics and analysis for variation graphs
  ☆39Updated 4 months ago
• CASTLE-Panel / castle
  CAncer Standards Long-read Evaluation
  ☆25Updated 2 months ago
• rlorigro / GFAse
  Tool for globally phasing diploid assembly graphs with orthogonal data
  ☆39Updated 5 months ago
• pierrepeterlongo / back_to_sequences
  ☆41Updated 2 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated 2 weeks ago
• lh3 / miniwfa
  A reimplementation of the WaveFront Alignment algorithm at low memory
  ☆49Updated 11 months ago
• TF-Chan-Lab / panGraphViewer
  Show pangenome graphs in an easy way
  ☆55Updated 2 years ago
• PacificBiosciences / jasmine
  Call select base modifications in PacBio HiFi reads
  ☆7Updated 3 months ago
• jts / smrest
  Tumour-only somatic mutation calling using long reads
  ☆26Updated 6 months ago
• human-pangenomics / hprc-tutorials
  ☆17Updated last year
• vikshiv / mumemto
  Mumemto: multi-MUM and MEM finding across pangenomes
  ☆79Updated 2 weeks ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆49Updated 5 years ago
• Psy-Fer / buttery-eel
  The buttery eel - a slow5 guppy/dorado basecaller wrapper
  ☆39Updated last month
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆89Updated 2 weeks ago
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆51Updated 2 years ago
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• PacificBiosciences / pb-human-wgs-workflow-snakemake
  DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
  ☆38Updated last year