nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

1. Read QC (FastQC or falco as an alternative option)
2. Performs optional read pre-processing
   • Adapter clipping and merging (short-read: fastp, AdapterRemoval2; long-read: porechop, Porechop_ABI)
   • Low complexity and quality filtering (short-read: bbduk, PRINSEQ++; long-read: Filtlong), Nanoq
   • Host-read removal (short-read: BowTie2; long-read: Minimap2)
   • Run merging
3. Supports statistics metagenome coverage estimation (Nonpareil) and for host-read removal (Samtools)
4. Performs taxonomic classification and/or profiling using one or more of:
   • Kraken2
   • MetaPhlAn
   • MALT
   • DIAMOND
   • Centrifuge
   • Kaiju
   • mOTUs
   • KrakenUniq
   • KMCP
   • ganon
5. Perform optional post-processing with:
   • bracken
6. Standardises output tables (Taxpasta)
7. Present QC for raw reads (MultiQC)
8. Plotting Kraken2, Centrifuge, Kaiju and MALT results (Krona)

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
2612,run1,ILLUMINA,2612_run1_R1.fq.gz,,
2612,run2,ILLUMINA,2612_run2_R1.fq.gz,,
2612,run3,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz,

Each row represents a fastq file (single-end), a pair of fastq files (paired end), or a fasta (with long reads).

Additionally, you will need a database sheet that looks as follows:

databases.csv:

tool,db_name,db_params,db_path
kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
metaphlan,db1,,/<path>/<to>/metaphlan/metaphlan_database/

That includes directories or .tar.gz archives containing databases for the tools you wish to run the pipeline against.

Now, you can run the pipeline using:

nextflow run nf-core/taxprofiler \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --databases databases.csv \
   --outdir <OUTDIR>  \
   --run_kraken2 --run_metaphlan

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

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.

nf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team.

• James A. Fellows Yates
• Sofia Stamouli
• Moritz E. Beber

We thank the following people for their contributions to the development of this pipeline:

• Lauri Mesilaakso
• Tanja Normark
• Maxime Borry
• Thomas A. Christensen II
• Jianhong Ou
• Rafal Stepien
• Mahwash Jamy
• Lily Andersson Lee

We also are grateful for the feedback and comments from:

• The general nf-core/community

And specifically to

• Alex Hübner

❤️ also goes to Zandra Fagernäs for the logo.

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 #taxprofiler channel (you can join with this invite).

If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: 10.1101/2023.10.20.563221.

Stamouli, S., Beber, M. E., Normark, T., Christensen II, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221

For the latest version of the code, cite the Zenodo doi: 10.5281/zenodo.7728364

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.