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Sofia Stamouli 2022-12-13 09:50:05 +01:00
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@ -174,6 +174,8 @@ nextflow run nf-core/taxprofiler --input samplesheet.csv --databases databases.c
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
When running nf-core/taxprofiler, every step and tool is 'opt in'. To run a given profiler you must make sure to supply both a database in your `<database>.csv` and supply `--run_<profiler>` flag to your command. Omitting either will result in the profiling tool not executing. If you wish to perform pre-processing (adapter clipping, merge running etc.) or post-processing (visualisation) steps, these are also opt in `--perform_<step>` and in some cases may also require additional files. Please check the parameters tab of this documentation for more information.
Note that the pipeline will create the following files in your working directory: Note that the pipeline will create the following files in your working directory:
```bash ```bash
@ -574,6 +576,14 @@ In addition to a Kraken2 database, you also need to have the (average) read leng
```bash ```bash
bracken-build -d <KRAKEN_DB_DIR> -k <KRAKEN_DB_KMER_LENGTH> -l <READLENGTH> bracken-build -d <KRAKEN_DB_DIR> -k <KRAKEN_DB_KMER_LENGTH> -l <READLENGTH>
```
> 🛈 You can speed up database construction by supplying the threads parameter (`-t`).
> 🛈 If you do not have Kraken2 in your `$PATH` you can point to the binary with `-x /<path>/<to>/kraken2`.
You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.shtml?t=manual) for more information. Alternatively, you can use one of the indexes that can be found [here](https://benlangmead.github.io/aws-indexes/k2).
#### KrakenUniq #### KrakenUniq
For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2). But if you wish to build your own, please see the [documentation](https://github.com/fbreitwieser/krakenuniq/blob/master/README.md#custom-databases-with-ncbi-taxonomy). For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2). But if you wish to build your own, please see the [documentation](https://github.com/fbreitwieser/krakenuniq/blob/master/README.md#custom-databases-with-ncbi-taxonomy).