Derrick Wood (@DerrickEWood) header
Derrick Wood (@DerrickEWood) profile picture

Derrick Wood

@DerrickEWood

Computer science and bioinformatics researcher

 Baltimore, MD
Joined December 2010
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Photo by Derrick Wood (@DerrickEWood)
I almost forgot to mention this, but our Kraken 2 paper was published on Thanksgiving in @GenomeBiology genomebiology.biomedcentral.… Thanks to @JenniferLu717 and @BenLangmead for all their work on the project, and to our reviewers for helping us make it a more informative paper!
Improved metagenomic analysis with Kraken 2

Improved metagenomic analysis with Kraken 2

Genome Biology - Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some...

link.springer.com
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For those interested in seeing a bit under the hood, I made this overview of the algorithm & data structure differences between Kraken 2 and Kraken 1. You can read the full details at biorxiv.org/content/10.1101/…
Image from Derrick Wood (@DerrickEWood)
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Use Kraken if you want a fast command line version of this method ccb.jhu.edu/software/kraken/ teapawt.net/sebhtml/status/6315561…
Sébastien Boisvert (@sebhtml) profile pictureSébastien Boisvert@sebhtml12 Aug 2015
One Codex and Microbiology's Search Problem - Bio-IT World bio-itworld.com/2015/2/9/one… #genomics #cloud
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Kraken 0.10.5-beta released ccb.jhu.edu/software/kraken - lower RAM build reqs, improved support for custom DBs and more
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Kraken 0.10.4-beta released ccb.jhu.edu/software/kraken/ - RNA virus genomes, simple confidence scoring & more
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Derrick Wood retweeted
Homolog.us (@homolog_us) profile picture
Homolog.us@homolog_us7 Mar 2014
Kraken - Very Good Application of Jellyfish and Minimizer (homolog.us/blogs/blog/2014/0…)
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Pretty impressed with speed and sensitivity of Steve Salzberg's Kraken on my data: ccb.jhu.edu/software/kraken/
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Our ultrafast metagenomic classifier Kraken (ccb.jhu.edu/software/kraken/) was published today in @GenomeBiology: genomebiology.com/2014/15/3/…
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