Introduction

nf-core/funcprofiler is a bioinformatics pipeline for read-based functional profiling of microbiome sequencing data. It accepts already preprocessed short-read FASTQ files and runs one or more functional profilers against user-supplied databases, producing gene family abundances, pathway abundances, pathway coverages, and antimicrobial resistance profiles. Long-read platforms are not supported in this release.

Pipeline Summary

Supported profilers and current status:

1. HUMANn v3 — functional profiling via MetaPhlAn + HUMANn 3 (--run_humann_v3)
2. HUMANn v4 — functional profiling via MetaPhlAn + HUMANn 4 (--run_humann_v4)
3. FMH FunProfiler — sketch-based functional profiling (--run_fmhfunprofiler)
4. RGI — antimicrobial resistance gene identification (--run_rgi, available)
5. mifaser — functional profiling via mifaser (--run_mifaser, available)
6. DIAMOND — alignment with DIAMOND blastx (--run_diamond, work in progress / beta)
7. eggNOG-mapper — functional annotation, orthology assignments and domain prediction (--run_eggnogmapper, work in progress / beta)

Usage

First, prepare a samplesheet with your input data:

samplesheet.csv:

sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
SAMPLE1,RUN1,ILLUMINA,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,
SAMPLE2,RUN1,ILLUMINA,/path/to/sample2.fastq.gz,,

Each row represents a sequencing run. Multiple rows with the same sample and different run_accession values will be merged before profiling. Reads are expected to arrive already preprocessed: the pipeline performs no read QC, trimming or host decontamination.

Then prepare a databases sheet — see docs/usage.md for the full format. Here is an abbreviated example for running HUMANn (which requires 4 databases):

databases.csv

tool,db_name,db_entity,db_params,db_path
humann_v3,uniref90_v3,humann_metaphlan,,/data/databases/metaphlan_db
humann_v3,uniref90_v3,humann_nucleotide,,/data/databases/chocophlan
humann_v3,uniref90_v3,humann_protein,,/data/databases/uniref90_diamond
humann_v3,uniref90_v3,humann_utility,,/data/databases/utility_mapping

Now, you can run the pipeline using:

nextflow run nf-core/funcprofiler \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --databases databases.csv \
   --run_humann_v3

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/funcprofiler was originally written by Nick Waters, Vini Salazar, Yixuan Yang, Mirae Baichoo.

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

• Matthias Hörtenhuber
• James Fellows Yates
• Jonas Scheid

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 #funcprofiler 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.