Alternatives and similar repositories for sapling:

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

• Kmer-File-Format / kff-tools
  ☆17Updated last year
• lh3 / miniwfa
  A reimplementation of the WaveFront Alignment algorithm at low memory
  ☆49Updated 10 months ago
• jeizenga / wfalm
  Refinements of the WFA alignment algorithm with better complexity
  ☆26Updated 3 years ago
• jermp / fulgor
  Fulgor is a fast and space-efficient colored de Bruijn graph index.
  ☆49Updated last week
• VGP / vgp-tools
  ☆28Updated last week
• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• ParBLiSS / PaSGAL
  Parallel Sequence to Graph Alignment
  ☆35Updated 2 years ago
• RagnarGrootKoerkamp / minimizers
  Reference implementations of minimizer schemes to go with the mod-minimizers paper.
  ☆24Updated last month
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 3 years ago
• pairwise-alignment / pa-bench
  Benchmarking pairwise aligners
  ☆36Updated 2 months ago
• bioinf-benchmarking / mapping-benchmarking
  Snakemake pipeline for benchmarking read mappers
  ☆16Updated last year
• jts / smrest
  Tumour-only somatic mutation calling using long reads
  ☆26Updated 5 months ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆38Updated 4 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
• ekg / HLA-zoo
  genome variation graphs constructed from HLA GRCh38 ALTs
  ☆23Updated 3 years ago
• maxrossi91 / moni
  MONI: A Pangenomic Index for Finding MEMs
  ☆37Updated 3 weeks ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆23Updated 2 months ago
• Kmer-File-Format / kff-reference
  Contains the description of a file format to store kmers and associated values
  ☆32Updated 2 years ago
• COMBINE-lab / piscem
  Rust wrapper for the next generation (still currently in C++)
  ☆24Updated 2 months ago
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆16Updated 6 years ago
• DecodeGenetics / LRcaller
  ☆16Updated 3 years ago
• lh3 / pubLRasm
  ☆17Updated 4 years ago
• Platinum-Pedigree-Consortium / Platinum-Pedigree-Datasets
  ☆18Updated 2 months ago
• kcleal / pywfa
  Python wrapper for wavefront alignment using WFA2-lib
  ☆35Updated 5 months ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• HongzheGuo / deBGA
  de Bruijn Graph-based read aligner
  ☆33Updated 6 years ago
• langmead-lab / vargas
  ☆25Updated 3 years ago
• jts / mbtools
  ☆14Updated last year
• lh3 / rmaxcut
  An experimental tool to find approximate max-cuts in a large graph
  ☆11Updated 3 years ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆28Updated 4 months ago