Introduction

nf-core/pathogenepidemiology is a bioinformatics pipeline that ...

1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))

Usage

Now, you can run the pipeline using:

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

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.

Pipeline input

To run this pipeline, you will need a reference genome for both your pathogen of interest, and its host.

We will patch this out before release, but pathogenepidemiology developers can get reference genome data with:

QUERY_GENOME="https://ftp.ebi.ac.uk/ensemblgenomes/pub/protists/release-62/fasta/plasmodium_falciparum/dna/Plasmodium_falciparum.GCA000002765v3.dna.toplevel.fa.gz"
HOST_GENOME="https://ftp.ebi.ac.uk/ensemblgenomes/pub/metazoa/release-62/fasta/anopheles_gambiae/dna/Anopheles_gambiae.AgamP4.dna.toplevel.fa.gz"

nextflow run workflows/download_references.nf -profile docker --validation_monochromeLogs false --queryurl $QUERY_GENOME --hosturl $HOST_GENOME

Credits

nf-core/pathogenepidemiology was originally written by Igiraneza Clement, Bilal Asser, Firas Zemzem, more tbc.

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

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 #pathogenepidemiology 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.