Alternatives and similar repositories for wfa

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

• broadinstitute / poasta
  Fast and exact gap-affine partial order alignment
  ☆55Updated 2 weeks ago
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 4 months ago
• kcleal / pywfa
  Python wrapper for wavefront alignment using WFA2-lib
  ☆37Updated 11 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆31Updated 3 weeks ago
• RagnarGrootKoerkamp / minimizers
  Reference implementations of minimizer schemes to go with the mod-minimizers paper.
  ☆26Updated 6 months ago
• pierrepeterlongo / back_to_sequences
  ☆45Updated last week
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆21Updated 6 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆25Updated 11 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 6 months ago
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆25Updated last week
• brianli314 / palindrome-finder
  A bioinformatics tool written in Rust to find palindromic sequences in DNA
  ☆35Updated last month
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated 10 months ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆26Updated this week
• cschin / wavefront-aln
  A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring
  ☆14Updated 2 years ago
• lijuzeng / dna2bit
  ☆12Updated 10 months ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated last year
• mlin / gfabase
  GFA insert into GenomicSQLite
  ☆49Updated 4 years ago
• MoinSebi / gfa2bin
  ☆25Updated 2 months ago
• tlemane / kmdiff
  Differential k-mer analysis
  ☆37Updated last year
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆27Updated last year
• mbhall88 / psdm
  Compute a pairwise SNP distance matrix from one or two alignment(s)
  ☆25Updated last year
• mbhall88 / pafpy
  A lightweight library for working with PAF (Pairwise mApping Format) files
  ☆30Updated 3 years ago
• jermp / fulgor
  ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.
  ☆55Updated 3 weeks ago
• imartayan / CBL
  A Rust library providing fully dynamic sets of k-mers with high locality
  ☆46Updated last year
• lh3 / gffio
  ☆32Updated 2 years ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆35Updated 4 months ago
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆46Updated last month
• AntonBankevich / jumboDB
  De Bruijn graph construction for large k.
  ☆17Updated 4 years ago