smagala/denver

Introduction

smagala/denver is a bioinformatics pipeline for analyzing Dengue virus (DENV) Illumina sequencing data. It maps reads against multiple serotype references (DENV1-4 plus sylvatic variants), generates consensus sequences, identifies intra-host variants (iSNVs), and produces quality control visualizations.

This pipeline is a ph-core compliant NextFlow port of the DENV_pipeline originally developed by Verity Hill & Chrispin Chaguza at the Grubaugh Lab.

Pipeline Steps

1. Read QC (FastQC)
2. Read mapping to multiple serotype references (BWA MEM)
3. Primer trimming (iVar trim)
4. Consensus sequence generation (iVar consensus)
5. Consensus alignment (MAFFT)
6. Serotype calling based on coverage threshold
7. Variant calling (iVar variants)
8. Depth profiling (bedtools genomecov)
9. QC visualization (variant plots, coverage summaries)
10. Aggregate reporting (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.

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

samplesheet.csv:

sample,fastq_1,fastq_2
DENV1_sample,DENV1_S1_L001_R1_001.fastq.gz,DENV1_S1_L001_R2_001.fastq.gz
DENV2_sample,DENV2_S2_L001_R1_001.fastq.gz,DENV2_S2_L001_R2_001.fastq.gz

Each row represents a paired-end sample for DENV analysis.

Reference Assets

Reference files (FASTA, BED) are managed externally. The default configuration expects assets in a sibling directory:

parent_directory/
├── denver/              # This pipeline
└── assets/
    └── denver/
        └── 1.0.0/
            └── references/
                ├── DENV1.fasta, DENV1.bed, ...
                └── refs.txt

To use a custom references location:

nextflow run smagala/denver --references_base /path/to/references

Now, you can run the pipeline using:

nextflow run smagala/denver \
   -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.

Credits

smagala/denver was originally written by smagala.

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.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.