Alternatives and similar repositories for CompactTree:

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

• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• jermp / lphash
  Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
  ☆43Updated last year
• jermp / fulgor
  Fulgor is a fast and space-efficient colored de Bruijn graph index.
  ☆46Updated last week
• balabanmetin / apples
  distance based phylogenetic placement
  ☆26Updated 11 months ago
• edawson / rkmh
  Classify sequencing reads using MinHash.
  ☆48Updated 4 years ago
• langmead-lab / vargas
  ☆25Updated 3 years ago
• prophyle / prophasm
  ProphAsm – a rapid computation of simplitigs directly from k-mer sets
  ☆26Updated last year
• Malfoy / Blight
  De Bruijn graph representation in low memory
  ☆36Updated 6 months ago
• Kmer-File-Format / kff-reference
  Contains the description of a file format to store kmers and associated values
  ☆32Updated 2 years ago
• benedictpaten / sonLib
  Small general purpose library for C and Python with focus on bioinformatics.
  ☆29Updated 2 years ago
• rvaser / rala
  Layout module for raw de novo genome assembly of long uncorrected reads.
  ☆21Updated 3 years ago
• ddiazdom / lcg
  Efficient, parallel compression for terabyte-scale data
  ☆38Updated 2 weeks ago
• kcleal / superintervals
  Fast interval intersection library
  ☆35Updated this week
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated 6 months ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• ocxtal / dozeu
  SIMD-parallel BLAST X-drop DP on sequence graphs
  ☆24Updated 8 months ago
• imartayan / CBL
  A Rust library providing fully dynamic sets of k-mers with high locality
  ☆44Updated 4 months ago
• medvedevgroup / TwoPaCo
  A fast constructor of the compressed de Bruijn graph from many genomes
  ☆40Updated 2 years ago
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆22Updated last year
• tlemane / kmtricks
  modular k-mer count matrix and Bloom filter construction for large read collections
  ☆78Updated 3 months ago
• rust-seq / minimizer-iter
  Iterate over minimizers of a DNA sequence
  ☆27Updated 6 months ago
• mbhall88 / psdm
  Compute a pairwise SNP distance matrix from one or two alignment(s)
  ☆24Updated 4 months ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆34Updated last year
• COMBINE-lab / kmers
  A bit-packed k-mer representation (and relevant utilities) for rust
  ☆47Updated 7 months ago
• broadinstitute / pyfrost
  Python bindings for Bifrost with a NetworkX compatible API
  ☆28Updated last year
• VGP / vgp-tools
  ☆28Updated last year
• edawson / mkmh
  Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
  ☆24Updated 4 years ago
• medvedevgroup / UST
  ☆25Updated 3 years ago
• Malfoy / NIQKI
  Next Index to Query Kmer Intersection
  ☆16Updated last year
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated last week