Published December 16, 2025
| Version v0.9.1
Software
Open
nf-illumina2lineage: A Nextflow pipeline for SARS-CoV-2 genome assembly and lineage analysis
Description
A reproducible and modular Nextflow pipeline for SARS-CoV-2 genome assembly and lineage analysis from Illumina paired-end sequencing data. The pipeline automates read quality control, reference-based mapping, primer clipping, variant calling, consensus generation, lineage assignment, and phylogenetic analysis. Developed as part of the SARS-2 Bioinformatics & Data Science course.
Notes
If you use this software in your research, please cite it using the metadata from this file.
Files
bibymaths/nf-illumina2lineage-v0.9.1.zip
Files
(3.7 MB)
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md5:0a6b4a0998d577fa3b52aed7ec2c3d33
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Additional details
Related works
- Is supplement to
- Software: https://github.com/bibymaths/nf-illumina2lineage/tree/v0.9.1 (URL)
Software
- Repository URL
- https://github.com/bibymaths/nf-illumina2lineage