Introduction

nf-core/phiflow is a bioinformatics pipeline that simultaneously characterize the microbial composition and host gene expression RNA sequencing samples. Given a list of samples from raw reads as input data (FASTQ) the pipeline performs several steps to produce two data matrices: Host gene expression matrix and Microbial composition matrix. These data matrices can help researchers to investigate the host transcriptome response under the presence of identified microbes and the association of microbial presence with specific host gene modules.

1. Read QC (fastp)
2. Read alignment to the human host genome (STAR)
3. Infer library strandedness (RSeQC)
4. Quantify host gene expression (subread:featureCounts)
5. Taxonomic profiling of host unmapped reads (Kraken2)
6. Calculate confidence scores from Kraken2 taxonomic profiling (Conifer)
7. Present summary of all previous processing steps (MultiQC)

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.

Now, you can run the pipeline using:

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

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, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the the results of a 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/phiflow was originally written by Icaro Castro.

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

Robert A. Petit III @rpetit3

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 #phiflow 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.