Pangenomics Benchmark & Workbench

  • Name
  • Last updated
  • bifrost
    Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
    BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data
  • BloomFilterTrie
    An alignment-free, reference-free and incremental data structure for colored de Bruijn graph with application to pan-genome indexing.
  • bloomtree
    No description provided.
  • bloomtree-allsome
    Sequence Bloom Trees with All/Some split
  • cobs
    COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
  • cortex
    reference free variant assembly
  • cuttlefish
    Building the compacted de Bruijn graph efficiently from references or reads.
  • gatb-core
    Core library of the Genome Analysis Toolbox with de-Bruijn graph
  • HowDeSBT
    Sequence Bloom Tree, supporting determined/how split filters
  • kcollections
    An efficient kmer data structure for genomic applications.
  • kmtricks
    modular k-mer count matrix and Bloom filter construction for large read collections
  • mantis
    Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
  • mccortex
    De novo genome assembly and multisample variant calling
  • rainbowfish
    A succinct colored dBG representation
    No description provided.
  • raptor
    A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
    REINDEER REad Index for abuNDancE quERy
  • SeqOthello
    SeqOthello supports fast coverage query and containment query.
  • splitsbt
    No description provided.
  • themisto
    Space-efficient pseudoalignment with a colored de Bruijn graph
  • VARI
    Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.