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nf-illumina2lineage   \n\n![GitHub last commit](https://img.shields.io/github/last-commit/bibymaths/nf-illumina2lineage) \n \n[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/) \n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15376065.svg)](https://doi.org/10.5281/zenodo.15376065)\n\nA reproducible and modular **Nextflow pipeline** for **SARS-CoV-2 genome assembly and lineage analysis** from Illumina paired-end sequencing data.\n\n## Overview\n\nThis pipeline automates:\n- Read quality control\n- Reference-based mapping\n- Primer clipping\n- Variant calling\n- Consensus generation\n- Lineage assignment\n- Phylogenetic analysis\n\nIt is based on best-practice tools and developed as part of the *SARS-2 Bioinformatics \u0026 Data Science* course by Freie Universität Berlin and the Robert Koch Institute.\n\n## Quickstart\n\n```bash\ngit clone https://github.com/bibymaths/nf-illumina2lineage.git\ncd nf-illumina2lineage\n````\n\n\u003e 💡 See [docs/quickstart.md](docs/quickstart.md) for full details.\n\n## Inputs\n\n* Illumina paired-end `.fastq.gz` files\n* SARS-CoV-2 reference genome (downloaded automatically)\n\n## Outputs\n\n* QC reports: FastQC, Fastp, MultiQC\n* BAM \u0026 VCF files\n* Consensus FASTA sequences\n* Pangolin lineage annotations\n* Phylogenetic tree (.treefile)\n\nFor a full output structure, see [docs/outputs.md](docs/outputs.md).\n\n## Dependencies\n\nManaged via `mamba` or `Docker`:\n\n* QC: `fastqc`, `fastp`, `multiqc`\n* Mapping: `minimap2`, `samtools`, `bamclipper`\n* Variant Calling: `freebayes`, `vcftools`, `bcftools`\n* Consensus: `vcfR`, `bcftools`, `president`\n* Lineage \u0026 MSA: `pangolin`, `mafft`, `iqtree`\n\n## Documentation\n\nComplete documentation is available under the `docs/` folder and rendered via [MkDocs](https://www.mkdocs.org/). Includes:\n\n* [Pipeline overview](docs/workflow.md)\n* [Process details](docs/processes.md)\n* [Parameters](docs/parameters.md)\n* [Container usage](docs/containers.md)\n* [Lineage QC](docs/lineage_qc.md)\n\n## License\n\nThis project is licensed under the **BSD 3-Clause License**. See [LICENSE](LICENSE).\n\n## Author\n\n**Abhinav Mishra**  \nEmail: [mishraabhinav@gmail.com](mailto:mishraabhinav@gmail.com)\n\n## Acknowledgments\n\nDeveloped during the [SARS-2 Bioinformatics \u0026 Data Science](https://github.com/rki-mf1/2023-SC2-Data-Science) course at FU Berlin \u0026 RKI, under guidance of **Max von Kleist** and **Martin Hölzer**.\n\n---\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fnf-illumina2lineage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbibymaths%2Fnf-illumina2lineage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fnf-illumina2lineage/lists"}