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paper: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46
software: http://ccb.jhu.edu/software/kraken/
1/ Get the sequences you want to check. Note that symlinks won’t work if too distant.
2/ Gunzip .gz files
3/ kraken --fastq-input R1.fq > sequences.kraken
4/ This output files is just numbers. To translate to names: kraken-translate sequences.kraken > sequences.labels
5/ Show IDs: less sequences.labels
6/ Get report: kraken-report sequences.kraken > sequences.kraken_report
7/ View report: less sequences.kraken_report