Representation of k-mer sets
  • ESS-Compress: compresses a set of k-mers for disk storage
  • ESS-Color: compresses a set of k-mers sets for disk storage, aka a colored de Bruijn graph
  • BCALM 2: de Bruijn graph compacation from reads
Whole-genome comparison
  • BubbZ: whole-genome homology mapping
  • SibeliaZ: multiple whole-genome alignment and locally collinear block reconstruction
  • TwoPaCo: de Bruijn graph construction from complete genomes
Long read processing
  • isONcorrect: error correction of ONT transcriptomic reads
  • isONclust: de novo clustering of long transcript reads into genes
  • IsoCon: deriving finished transcript sequences from Iso-Seq reads
  • ESKEMAP: Exact SKEtch-based read MAPping
Chromosome Y data analysis
  • AmpliCoNE: Ampliconic Copy Number Estimator
  • RecoverY : classification of Y-chromosome specific reads (no longer maintained)
  • DiscoverY: Y-contig identification from whole genome assemblies (no longer maintained)
K-mer search
  • PLA-index: lightweight index for speeding up queries to a sorted list of k-mers.
  • HowDe-SBT : querying long strings in sequencing experiments.
  • AllSome-SBT: (deprecated, use HowDe-SBT  instead)
SNP genotyping and comparison
  • VarGeno: SNP genotyping from whole genome sequencing data.
  • VarMatch: matching variants in VCF files.
Sequence assembly
  • KmerGenie: k-mer size selection for genome assembly
  • UST: build a spectrum-preserving string set representation of a set of k-mers. This software has been subsumed by ESS-Compress
  • Hammer: error-correction of high-throughput sequencing datasets (deprecated)
  • FlowgramFixer: base-caller for IonTorrent sequencing data (deprecated)
  • CNVer: method for detecting copy number variation (deprecated)

Note: some additional software not listed here is hosted on our group’s GitHub home.