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- RecoverY : classification of Y-chromosome specific reads (no longer maintained)
- DiscoverY: Y-contig identification from whole genome assemblies (no longer maintained)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 database search
- 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
Miscellaneous
- Confidence intervals computation for k-mer sequences
- Bidirected network flow solver (download) (not supported).
Deprecated
- 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.