Alternatives and similar repositories for pa-bench

Users that are interested in pa-bench are comparing it to the libraries listed below

• rust-seq / minimizer-iter
  Iterate over minimizers of a DNA sequence
  ☆31Updated last year
• broadinstitute / poasta
  Fast and exact gap-affine partial order alignment
  ☆54Updated last month
• jermp / fulgor
  ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.
  ☆52Updated this week
• RagnarGrootKoerkamp / minimizers
  Reference implementations of minimizer schemes to go with the mod-minimizers paper.
  ☆25Updated 4 months ago
• rchikhi / rust-alignbench
  Pairwise nucleotide alignment benchmark of Rust bindings
  ☆31Updated 2 years ago
• kcleal / pywfa
  Python wrapper for wavefront alignment using WFA2-lib
  ☆35Updated 9 months ago
• lh3 / lv89
  C implementation of the Landau-Vishkin algorithm
  ☆35Updated 3 years ago
• lh3 / miniwfa
  A reimplementation of the WaveFront Alignment algorithm at low memory
  ☆50Updated last year
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• natir / rustyread
  A long read simulator based on badread idea
  ☆23Updated 2 years ago
• AlgoLab / RecGraph
  Optimal sequence-to-graph alignment with recombinations
  ☆36Updated last month
• jts / smrest
  Tumour-only somatic mutation calling using long reads
  ☆27Updated 9 months ago
• biointec / browniealigner
  Alignment algorithm for short Illumina reads to a de Bruijn graph
  ☆16Updated 6 years ago
• vgteam / libbdsg
  Optimized sequence graph implementations for graph genomics
  ☆34Updated this week
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆24Updated 2 months ago
• shenwei356 / wfa
  Wavefront alignment algorithm (WFA) in Golang
  ☆30Updated last month
• pangenome / impg
  implicit pangenome graph
  ☆67Updated last week
• COMBINE-lab / piscem
  Rust wrapper for the next generation (still currently in C++)
  ☆28Updated last month
• moold / kseq-rs
  A FASTA/FASTQ format parser library
  ☆20Updated last year
• Kmer-File-Format / kff-reference
  Contains the description of a file format to store kmers and associated values
  ☆32Updated 3 years ago
• jeizenga / wfalm
  Refinements of the WFA alignment algorithm with better complexity
  ☆26Updated 3 years ago
• imartayan / CBL
  A Rust library providing fully dynamic sets of k-mers with high locality
  ☆45Updated 10 months ago
• natir / biotest
  Generate random test data for bioinformatics
  ☆26Updated last year
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆23Updated last week
• chfi / rs-wfa
  Rust bindings to the wavefront algorithm C implementation
  ☆18Updated 2 years ago
• ekg / HLA-zoo
  genome variation graphs constructed from HLA GRCh38 ALTs
  ☆23Updated 3 years ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated last month
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆37Updated 2 months ago
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆25Updated 9 months ago