WorkingDogs
The home repo for the Working Dogs bioinformatics tools: Blue, Pup, Kelpie and other members of the pack. These tools are all kMer-based and make use of the very useful almost-always-unique properties of moderate-length kMers (k=20+).
Blue is a DNA read error corrector based on kMers and their context. It was published as "Blue: correcting sequencing errors using consensus and context" in Bioinformatics. 2014; 30(19), 2723-2732. Release 2.0 appeared here around the middle of 2018.
Pup is a kMer-based gene/genome comparator uses techniques from error correction to get better-than-BLAST similarity numbers for sequences ranging from genes to whole genomes. It will be published after Kelpie_v2.
Kelpie is a specialised assembler for between-primer regions, taking WGS reads and producing the equivalent of amplicons. It was published in PeerJ in January 2019. https://peerj.com/articles/6174/
Kelpie_v2 is the latest release of Kelpie, providing both new features and improved performance/efficacy. Unfiltered WGS reads files can now be used directly, although pre-filtering reads is still recommended where possible for performance reasons. Much of the code is now multi-threaded as well. Accuracy and the ability to extract/assemble very low abundance sequences have also been improved.
FilterReads is a boringly-named kMer filter than can rapidly find reads of interest in very large datasets. Given a 16S filter, it produces results very similar to HMM-based tools, but runs at close to IO speed.
Other kMer-based bioiformatics tool will join the pack from time to time.