nf-illumina2lineage

A Nextflow pipeline for SARS-CoV-2 genome assembly and lineage assignment from Illumina paired-end sequencing data.

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Quickstart

git clone https://github.com/bibymaths/nf-illumina2lineage.git
cd nf-illumina2lineage
nextflow run main.nf

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Documentation

All documentation lives in docs/ and is rendered here.

• Getting started: docs/quickstart.md
• Workflow overview: docs/workflow.md
• Processes: docs/processes.md
• Parameters: docs/parameters.md
• Outputs: docs/outputs.md
• Lineage QC: docs/lineage_qc.md

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Inputs

• Illumina paired-end FASTQ.gz
• SARS-CoV-2 reference genome (auto-downloaded)

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Outputs

• QC reports (FastQC, Fastp, MultiQC)
• BAM and VCF files
• Consensus FASTA
• Pangolin lineage assignments
• Phylogenetic tree

See docs/outputs.md for details.

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License

BSD 3-Clause License. See LICENSE.

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Author

Abhinav Mishra Email: mishraabhinav@gmail.com

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Acknowledgments

Developed during the SARS-2 Bioinformatics and Data Science course at Freie Universität Berlin and the Robert Koch Institute.

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