Kraken

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