Alternatives and similar repositories for r-index:

Users that are interested in r-index are comparing it to the libraries listed below

• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• VGP / vgp-tools
  ☆28Updated last week
• isovic / minialign
  Minimalistic aligner which uses Minimap for input mapping locations and Edlib for fast bitvector alignment.
  ☆10Updated 7 years ago
• Kmer-File-Format / kff-reference
  Contains the description of a file format to store kmers and associated values
  ☆32Updated 2 years ago
• RagnarGrootKoerkamp / minimizers
  Reference implementations of minimizer schemes to go with the mod-minimizers paper.
  ☆24Updated last month
• langmead-lab / vargas
  ☆25Updated 3 years ago
• bede / kindel
  Indel-aware consensus for aligned BAM
  ☆21Updated 3 weeks ago
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆16Updated 6 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 5 months ago
• bioinf-benchmarking / mapping-benchmarking
  Snakemake pipeline for benchmarking read mappers
  ☆16Updated last year
• rust-seq / minimizer-iter
  Iterate over minimizers of a DNA sequence
  ☆28Updated 9 months ago
• lh3 / pubLRasm
  ☆17Updated 4 years ago
• pairwise-alignment / pa-bench
  Benchmarking pairwise aligners
  ☆36Updated 2 months ago
• HongzheGuo / deBGA
  de Bruijn Graph-based read aligner
  ☆33Updated 6 years ago
• rcedgar / syncmer
  Validation of sycnmers compared to minimizers
  ☆11Updated 4 years ago
• cvdelannoy / poreTally
  Benchmark MinION assembler pipelines and publish your results in a heartbeat!
  ☆15Updated 5 years ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years 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 / miniwfa
  A reimplementation of the WaveFront Alignment algorithm at low memory
  ☆49Updated 10 months ago
• AntonBankevich / jumboDB
  De Bruijn graph construction for large k.
  ☆18Updated 3 years ago
• ParBLiSS / PaSGAL
  Parallel Sequence to Graph Alignment
  ☆35Updated 2 years ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆37Updated last year
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆23Updated 2 months ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 4 years ago
• natir / rustyread
  A long read simulator based on badread idea
  ☆22Updated 2 years ago
• mchaisso / mcutils
  ☆12Updated 3 years ago
• mbhall88 / pafpy
  A lightweight library for working with PAF (Pairwise mApping Format) files
  ☆31Updated 2 years ago
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆33Updated 4 years ago
• TavorB / spectral_jaccard_similarity
  ☆14Updated 2 years ago