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1 Abstract27
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3 Description135
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--help
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4 Discussion181
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6 Code Availability262
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7 Acknowledgments268
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8 Funding273
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9 Conict of Interest Statement283
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10 Supplementary Information288
10.1 Implementation289
10.1.1 Input and Execution290
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Listing 1
$nextflow run nf-core/taxprofiler \
-r 1.1.0 \
-profile singularity,<institute> \
--input <samplesheet.csv> \
--databases <database.csv> \
--perform_shortread_qc \
--shortread_qc_minlength 20 \
--preprocessing_qc_tool falco \
--run_host_removal --hostremoval_reference 'host_genome.fasta' \
--run_kraken2 --kraken2_save_reads \
--run_metaphlan \
--run_krona \
--run_profile_standardisation
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--run_kraken2
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-r
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10.1.3 Proling375
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--run_<tool>
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