• SibeliaZ: multiple whole-genome alignment and locally collinear block reconstruction.
  • isONclust: de novo clustering of long transcript reads into genes
  • IsoCon: deriving finished transcript sequences from Iso-Seq reads.
  • HowDe-SBT : querying long strings in sequencing experiments.
  • VarGeno: SNP genotyping from whole genome sequencing data.
  • RecoverY : classification of Y-chromosome specific reads
  • DiscoverY: Y-contig identification from whole genome assemblies
  • VarMatch : matching variants in VCF files.
  • BCALM 2: de Bruijn graph compacation from reads.
  • TwoPaCo: de Bruijn graph construction from complete genomes.
  • KmerGenie: k-mer size selection for genome assembly
  • Hammer: error-correction of high-throughput sequencing datasets
  • Bidirected network flow solver (download).
  • 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.