Derrick Wood

Computer science and bioinformatics researcher

[Derrick Wood @DerrickEWood]

@remkv6_rick @isugif @GenomeBiology @JenniferLu717 @BenLangmead This would mean that the read data has at least a few matches to some part of the human genome. If the ref. region getting hit is very small, that could indicate false positives or maybe some sort of sample contamination. Hard to diagnose here - pls email if you want to follow up

[Derrick Wood @DerrickEWood]

I almost forgot to mention this, but our Kraken 2 paper was published on Thanksgiving in @GenomeBiology https://t.co/mPOLgYvAyw 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!

[Derrick Wood @DerrickEWood]

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 https://t.co/iwyXXBiARd

[Torsten Seemann @torstenseemann]

Use Kraken if you want a fast command line version of this method
https://t.co/9h1Beq5QV8 https://t.co/LWZqR5WqVk

[Derrick Wood @DerrickEWood]

@KristaTernus Awesome :) Hadn't heard of KoT, will have to check it out.

[Derrick Wood @DerrickEWood]

@bioinformer Glad you like it - hope it's useful. Just FYI, that's actually been available since the 0.10.5 release.

[Derrick Wood @DerrickEWood]

@bioinformer DBs are compatible, no need to rebuild

[Derrick Wood @DerrickEWood]

@bioinformer accuracy is the same, memory reduced for build process (not runtime DB) by using I/O lib calls in place of greedy mmap

[Derrick Wood @DerrickEWood]

Kraken 0.10.5-beta released http://t.co/Vs1ckysReV - lower RAM build reqs, improved support for custom DBs and more

[Derrick Wood @DerrickEWood]

@jjsso0 Yes, but if you want detection of things outside of bacteria/archaea/viruses, you'll need to make a custom DB

[Derrick Wood @DerrickEWood]

@nomad421 Have you had any problems/complaints in requiring C++11 support for Sailfish?

[Derrick Wood @DerrickEWood]

Kraken 0.10.4-beta released http://t.co/Ursk3tYkvo - RNA virus genomes, simple confidence scoring & more

[Homolog.us @homolog_us]

Kraken - Very Good Application of Jellyfish and Minimizer (http://t.co/ZmyuOOJhVq)

[Nick Loman @pathogenomenick]

Pretty impressed with speed and sensitivity of Steve Salzberg's Kraken on my data: http://t.co/7WDl92e8Ki

[Derrick Wood @DerrickEWood]

@tadKeys Thanks!

[Derrick Wood @DerrickEWood]

@KristaTernus @bnfojoe Thanks! Glad to hear you're both having good experiences with Kraken.

[Derrick Wood @DerrickEWood]

@nomad421 Thanks, Rob - I'm looking at taking an idea or two from Sailfish to make Kraken even faster in the future.

[Derrick Wood @DerrickEWood]

Our ultrafast metagenomic classifier Kraken (http://t.co/hgKcPDiFKG) was published today in @GenomeBiology: http://t.co/kH9zkNQh3i