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Classification accuracy and speed comparison of variants of Kraken for three simulated metagenomes. For each metagenome, genus precision and sensitivity are shown for five classifiers, and speed is shown for Kraken, along with a reduced memory version of Kraken (MiniKraken), quick execution versions of both (Kraken-Q and MiniKraken-Q), and Kraken run with a database containing draft and completed microbial genomes from GenBank (Kraken-GB). Results shown are for the same metagenomes used in Figure 2. Note that the scales of the axes differ from Figure 2, as the precision and speed of Kraken (and its variants) exceed that of the other classifiers used. (a) HiSeq metagenome. (b) MiSeq metagenome. (c) simBA-5 metagenome.
Although Kraken-GB does have higher sensitivity than Kraken, it sometimes makes surprising errors, which we discovered were caused by contaminant and adapter sequences in the contigs of some draft genomes. These contaminant sequences come from other bacteria, viruses or even human genomes, and they result in incorrectly labelled k-mers in the database. We attempted to remove these from Kraken-GB (Materials and methods), but some contaminants may still slip through any filters. Thus for now, the default version of Kraken uses only complete RefSeq genomes.
Kraken is written in C++ and Perl, and is available for download at [25] along with the metagenome data used to evaluate the accuracy of the classifiers presented here, and a downloadable 4-GB MiniKraken database similar to the one used here. The source code is also available from GitHub [26].
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