This repository contains a Nextflow-based bioinformatics pipeline for the analysis of Nanopore sequencing data.
- Adapter trimming using Porechop
- Alignment to a reference genome with Minimap2
- Variant calling with Bcftools
- Consensus sequence generation with iVar
The pipeline is dependent on the following software:
- Nextflow
- Docker
The required bioinformatics tools (Porechop, Minimap2, Samtools, Bcftools, iVar) are encapsulated within Docker containers, which are automatically fetched at runtime.
Ensure that both Nextflow and Docker are installed on your system.
To run the pipeline, use the following command:
nextflow run main.nf --reads '/path/to/reads/*.fastq' --ref '/path/to/reference.fasta' --outdir 'output_directory' -profile docker