Alternatives and similar repositories for ksw2

Users that are interested in ksw2 are comparing it to the libraries listed below

• lh3 / minimap
  This repo is DEPRECATED. Please use minimap2, the successor of minimap.
  ☆106Updated 7 years ago
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆172Updated last year
• ksahlin / strobealign
  Aligns short reads using dynamic seed size with strobemers
  ☆175Updated this week
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆141Updated last year
• smarco / WFA-paper
  Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
  ☆200Updated 3 years ago
• yangao07 / abPOA
  abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
  ☆126Updated last month
• human-pangenomics / HPP_Year1_Assemblies
  Assemblies from HPP Year 1 production
  ☆76Updated 2 years ago
• ocxtal / libgaba
  Adaptive semi-global banded alignment on string graphs
  ☆67Updated 7 years ago
• thegenemyers / FASTK
  A fast K-mer counter for high-fidelity shotgun datasets
  ☆131Updated 2 months ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆138Updated 2 months ago
• maickrau / GraphAligner
  ☆272Updated last month
• marbl / HG002
  A complete diploid human genome
  ☆125Updated this week
• cschin / Peregrine
  Peregrine: Fast Genome Assembler Using SHIMMER Index
  ☆102Updated 3 years ago
• lh3 / kmer-cnt
  Code examples of fast and simple k-mer counters for tutorial purposes
  ☆171Updated 5 years ago
• pangenome / odgi
  Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
  ☆219Updated last month
• ekg / seqwish
  alignment to variation graph inducer
  ☆150Updated last month
• human-pangenomics / hpp_pangenome_resources
  ☆117Updated last year
• yukiteruono / pbsim3
  PBSIM3: a simulator for all types of PacBio and ONT long reads
  ☆80Updated 4 months ago
• refresh-bio / agc
  Assembled Genomes Compressor
  ☆168Updated 9 months ago
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆101Updated 8 months ago
• GFA-spec / GFA-spec
  Graphical Fragment Assembly (GFA) Format Specification
  ☆213Updated last year
• lbcb-sci / graphmap2
  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…
  ☆68Updated 3 years ago
• marbl / MashMap
  A fast approximate aligner for long DNA sequences
  ☆282Updated 10 months ago
• smarco / WFA2-lib
  WFA-lib: Wavefront alignment algorithm library v2
  ☆190Updated 3 months ago
• mcveanlab / mccortex
  De novo genome assembly and multisample variant calling
  ☆113Updated 6 years ago
• nanoporetech / scrappie
  Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
  ☆93Updated 3 years ago
• lh3 / ropebwt3
  BWT construction and search
  ☆117Updated last month
• Psy-Fer / SquiggleKit
  SquiggleKit: A toolkit for manipulating nanopore signal data
  ☆126Updated last year
• lh3 / yak
  Yet another k-mer analyzer
  ☆144Updated last year
• twolinin / longphase
  ☆116Updated last week