Alternatives and similar repositories for seqan3

Users that are interested in seqan3 are comparing it to the libraries listed below

• seqan / seqan
  SeqAn's official repository.
  ☆495Updated 2 weeks ago
• pmelsted / bifrost
  Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
  ☆219Updated last week
• mengyao / Complete-Striped-Smith-Waterman-Library
  ☆310Updated 3 weeks ago
• jeffdaily / parasail
  Pairwise Sequence Alignment Library
  ☆264Updated 3 weeks ago
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆879Updated this week
• smarco / WFA2-lib
  WFA-lib: Wavefront alignment algorithm library v2
  ☆193Updated 4 months ago
• lh3 / cgranges
  A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
  ☆168Updated last year
• lh3 / kmer-cnt
  Code examples of fast and simple k-mer counters for tutorial purposes
  ☆170Updated 5 years ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆654Updated 2 months ago
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆171Updated last year
• BenLangmead / bowtie
  An ultrafast memory-efficient short read aligner
  ☆264Updated 3 years ago
• lh3 / minigraph
  Sequence-to-graph mapper and graph generator
  ☆456Updated last month
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆512Updated last year
• smarco / WFA-paper
  Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
  ☆199Updated 3 years ago
• marbl / MashMap
  A fast approximate aligner for long DNA sequences
  ☆281Updated 11 months ago
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆322Updated 5 months ago
• GFA-spec / GFA-spec
  Graphical Fragment Assembly (GFA) Format Specification
  ☆214Updated last year
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆635Updated 2 years ago
• NVlabs / nvbio
  NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.
  ☆219Updated 5 years ago
• refresh-bio / KMC
  Fast and frugal disk based k-mer counter
  ☆300Updated 2 months ago
• ruanjue / wtdbg2
  Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
  ☆528Updated last year
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆690Updated 2 weeks ago
• ratschlab / metagraph
  Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
  ☆125Updated 3 weeks ago
• mummer4 / mummer
  Mummer alignment tool
  ☆524Updated 7 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆830Updated last year
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆227Updated 3 months ago
• chanzuckerberg / shasta
  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
  ☆273Updated 2 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆460Updated this week
• maickrau / GraphAligner
  ☆271Updated last month
• pangenome / odgi
  Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
  ☆220Updated 2 months ago