Home repo for the Working Dogs pack of bioinformatics tools
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Blue
BuildFilter
FilterReads
Kelpie
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WorkingDogsCoreLibrary
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Correcting reads with Blue v2.pdf
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README.md

README.md

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 will appear 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 from genes to genomes. It will be published latr in 2018 (after Kelpie).

Kelpie is a specialised assembler for between-primer regions, taking WGS reads and producing the equivalent of amplicons. The publication is in the final stages of preparation.

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.