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Welcome to the documentation for the nf-illumina2lineage pipeline.

Overview

This repository provides a complete pipeline for assembling and analyzing the genome of SARS-CoV-2 using Illumina paired-end sequencing data. It includes steps for quality control, mapping, variant calling, primer clipping, consensus sequence generation, lineage annotation, and phylogenetic analysis.

Key Features

• Automated environment setup using pixi
• Comprehensive quality control with fastqc and fastp
• Mapping and visualization using minimap2, samtools, and IGV
• Primer sequence clipping for clean alignments
• Variant calling with freebayes
• Consensus sequence generation and lineage assignment with pangolin
• Phylogenetic analysis and multiple sequence alignment with mafft and iqtree
• Clear documentation and modular structure

System Requirements

• Operating System: Linux (tested on Fedora 38)
• Processor: Intel i5 or higher, with multithreading support
• Memory: Minimum 8 GB

Dependencies

The pipeline requires the following tools, managed via mamba:

• QC: fastqc, fastp, multiqc
• Mapping: minimap2, samtools, bamclipper
• Variant Calling: freebayes, vcftools, bcftools
• Sequence Analysis: mafft, iqtree, pangolin
• Visualization: IGV

Input Data

• Illumina paired-end sequencing data
• SARS-CoV-2 reference genome (NCBI accession: NC_045512.2)

Output

• Quality control reports (.html, .json)
• Aligned sequences in BAM and VCF formats
• Consensus sequences in FASTA format
• Lineage annotations
• Phylogenetic trees and visualizations