# nf-core/createtaxdb

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1. Prepares input FASTA files for building 2. Builds databases for: - [Bracken](https://doi.org/10.7717/peerj-cs.104) - [Centrifuge](https://doi.org/10.1101/gr.210641.116) - [DIAMOND](https://doi.org/10.1038/nmeth.3176) - [ganon](https://doi.org/10.1093/bioinformatics/btaa458) - [Kaiju](https://doi.org/10.1038/ncomms11257) - [KMCP](https://doi.org/10.1093/bioinformatics/btac845) - [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) - [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0) - [MALT](https://doi.org/10.1038/s41559-017-0446-6) ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare an input CSV table with your input reference genomes that looks as follows: ```csv id,taxid,fasta_dna,fasta_aa Human_Mitochondrial_genome,9606,chrMT.fna, SARS-CoV-2_genome,694009,GCA_011545545.1_ASM1154554v1_genomic.fna.gz,GCA_011545545.1_ASM1154554v1_genomic.faa.gz Bacteroides_fragilis_genome,817,GCF_016889925.1_ASM1688992v1_genomic.fna.gz,GCF_016889925.1_ASM1688992v1_genomic.faa.gz Candidatus_portiera_aleyrodidarum_genome,91844,GCF_000292685.1_ASM29268v1_genomic.fna,GCF_000292685.1_ASM29268v1_genomic.faa Haemophilus_influenzae_genome,727,GCF_900478275.1_34211_D02_genomic.fna,GCF_900478275.1_34211_D02_genomic.faa Streptococcus_agalactiae_genome,1311,,GCF_002881355.1_ASM288135v1_genomic.faa ``` Each row contains a human readable name, the taxonomic ID of the organism, and then an (optionally gzipped) Nucleotide and/or Amino Acid FASTA file. Now, with an appropriate set of taxonomy files you can build databases for multiple profilers - such as Kraken2, ganon, and DIAMOND - in parallel: ```bash nextflow run nf-core/createtaxdb \ -profile \ --input samplesheet.csv \ --accession2taxid ///taxonomy/nucl_gb.accession2taxid \ --nucl2taxid ///taxonomy/nucl.accession2taxid.gz \ --prot2taxid ///taxonomy/prot.accession2taxid.gz \ --nodesdmp ///taxonomy/nodes.dmp \ --namesdmp ///taxonomy/names.dmp \ --build_kraken2 \ --kraken2_build_options='--kmer-len 45' \ --build_ganon \ --ganon_build_options='--kmer-size 45' \ --build_diamond \ --diamond_build_options='--no-parse-seqids' \ --outdir ``` The output directory will contain directories containing the database files for each of the profilers you selected to build. Optionally you can also package these as `tar.gz` archives. You can also generate pre-prepared input sheets for database specifications of pipelines such as [nf-core/taxprofiler](https://nf-co.re/taxprofiler) using `--generate_downstream_samplesheets`. > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/createtaxdb/usage) and the [parameter documentation](https://nf-co.re/createtaxdb/parameters). ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/createtaxdb/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/createtaxdb/output). ## Credits nf-core/createtaxdb was originally written by James A. Fellows Yates, Sam Wilkinson, Alexander Ramos Díaz, Lili Andersson-Li and the nf-core community. We thank the following people for their extensive assistance in the development of this pipeline: - Zandra Fagernäs for logo design ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#createtaxdb` channel](https://nfcore.slack.com/channels/createtaxdb) (you can join with [this invite](https://nf-co.re/join/slack)). ## Citations An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

License
  MIT

## Contents

- ["nf-core/createtaxdb"]
- assets/
- conf/
- docs/
- docs/images/
- modules/
- modules/local/
- modules/nf-core/
- workflows/
- subworkflows/
- nextflow.config
- README.md
- nextflow_schema.json
- CHANGELOG.md
- LICENSE
- CODE_OF_CONDUCT.md
- CITATIONS.md
- modules.json
- docs/usage.md
- docs/output.md
- .nf-core.yml
- .pre-commit-config.yaml
- .prettierignore