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Add explicit sentnece about classification/profiling

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James Fellows Yates 2023-01-17 15:23:59 +01:00
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docs/usage.md
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@ -201,7 +201,13 @@ You can optionally save the FASTQ output of the run merging with the `--save_run
#### Classification and Profiling
The following suggestion gives you some tips and suggestions regarding running some of the different tools specifically _within the pipeline_. For advice as to which tool to run in your context, please see the documentation of each tool.
The following suggestion gives you some tips and suggestions regarding running some of the different tools specifically _within the pipeline_.
An important distinction between the different tools in included in the pipeline is classification versus profiling. Taxonomic _classification_ is concerned with simply detecting the presence of species in a given sample. Taxonomic _profiling_ involves additionally estimating the _abundance_ of each species.
Note that not all taxonomic classification tools (e.g. Kraken, MALT, Kaiju) performs _profiling_, but all taxonomic profilers (e.g. MetaPhlAn, mOTUs, Bracken) must perform some form of _classification_ prior to profiling.
For advice as to which tool to run in your context, please see the documentation of each tool.
###### Bracken