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.

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

Usage

First, prepare an input CSV table 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. 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 using --generate_downstream_samplesheets.

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.

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.

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

Citations

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.