Introduction

nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input reference genome set in a highly automated and parallelised manner. It supports both nucleotide and protein based classifiers and profilers. The pipeline is designed to be a companion pipeline to nf-core/taxprofiler for taxonomic profiling of metagenomic data, but can be used for any context.

1. Prepares input FASTA files for building
2. Builds databases for:
   • Bracken
   • Centrifuge
   • DIAMOND
   • ganon
   • Kaiju
   • KMCP
   • Kraken2
   • KrakenUniq
   • MALT
   • sourmash
   • sylph

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare an input comma-separated table (csv) with your input reference genomes that looks as follows:

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:

nextflow run nf-core/createtaxdb \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --accession2taxid /<path>/<to>/taxonomy/nucl_gb.accession2taxid \
   --nucl2taxid /<path>/<to>/taxonomy/nucl.accession2taxid.gz \
   --prot2taxid /<path>/<to>/taxonomy/prot.accession2taxid.gz \
   --nodesdmp /<path>/<to>/taxonomy/nodes.dmp \
   --namesdmp /<path>/<to>/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 <OUTDIR>

The output directory will contain directories containing the database files for each of the profilers you selected to build.

You can also generate pre-prepared input sheets for database specifications of pipelines such as nf-core/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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

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.

It has been extended by Moritz Beber (@Midnighter; adding sourmash support).

We thank the following people for their extensive assistance in the development of this pipeline:

• Zandra Fagernäs (@ZandraFagernas) for logo design
• Paul Cantalupo (@pcantalupo) for additional documentation

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #createtaxdb channel (you can join with this invite).

Citations

If you use nf-core/createtaxdb for your analysis, please cite it using the following doi: 10.5281/zenodo.15696114

An extensive list of references for the tools used by the pipeline can be found in the 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.