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Note: Under the System Requirements within the Dependencies section, it talks about Multithreading is handled using OpenMP. ... Unlike Kraken 1, Kraken 2 does not use an external k-mer counter. However, by default, Kraken 2 will attempt to use the dustmasker or segmasker programs provided as part of NCBI's BLAST suite to mask low-complexity regions (see Masking of Low-complexity Sequences).
Multicore
The kraken2 application can run across multiple threads. Look at the commands usage bkraken2 -h for further details on the --threads option.
Example
Example based on Standard Kraken 2 Database. With respect to the above, you'll notice in the example below that it also uses the gpu-blast/1.1
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Teton:
gpu-blast/1.1Beartooth:
blast-plus/2.13.0
Kraken Databases
There are a number of reference database resources available, and we are happy to extend this list as researchers find useful links. Please email useful resources to arcc-help@uwyo.edu
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| Code Block |
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kraken2 -db ~/SupportingData/kraken2/k2_pluspfp_20210127 \ --threads 32 \ Starter_examples-246915672/SMS2_S2_L001_R1_001.fastq.gz Starter_examples-246915672/SMS2_S2_L001_R2_001.fastq.gz \ --use-names --minimum-base-quality 25 --confidence 0.5 \ --report 05SMS2ReportConf25.txt --output xxx.txt |
Issues
rsync vs ftp
Under the hood, kraken2 uses rsync to download data. During testing we have experienced various issues while downloading databases.
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