Derrick Wood, Jennifer Lu and Ben Langmead posted a preprint describing the Kraken 2 software tool, written by Derrick. Compared to the popular metagenomics read classification tool, Kraken 1, Kraken 2’s memory usage is several-fold smaller, allowing more reference genomes to be used at once. Kraken 2 is about 5-fold faster than Kraken 1, and adds a translated search mode for better sensitivity when classifying viruses. Like Kraken, Kraken 2 works well with the Bracken tool for abundance estimation. Please take a look and let us know of any software issues in Kraken 2 GitHub issues section.
Derrick was a Postdoctoral Fellow in the Langmead Lab in 2014–2015, and is now a Principal Scientist at Personal Genome Diagnostics in Baltimore. Jennifer is a PhD student with Steven Salzberg at JHU.