Home repo for the Working Dogs pack of bioinformatics tools
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
Correcting reads with Blue v2.pdf



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.