amplicon-nfamplicon-nf is a Nextflow pipeline for assembling consensus genomes and performing quality control on sequencing reads generated with ARTIC-style viral amplicon schemes. This configuration supports Illumina paired-end reads and Oxford Nanopore single FASTQ files, including mixed Illumina and Nanopore samples in the same run.Versions

v0.11.0 (default)

Tags: bioinformatics, viral genomics, amplicon sequencing, ARTIC, Nextflow, Illumina, Oxford Nanopore, consensus assemblyParameters

reads (file, multiple) required: Sequencing reads. Upload Illumina R1 and R2 files together as a pair. Individual FASTQ or FASTQ.GZ files are assumed to be Oxford Nanopore samples. Multiple paired and single-file samples can be supplied together.

scheme_mode (enum) required: Use a named scheme fetched and cached from the Quick Lab primerschemes repository, or upload a custom primer BED and reference FASTA. Options: named, custom

scheme_name (enum) required: Named PrimalScheme identifier. Used only when scheme_mode is named. Options: artic-bdbv-2026/400/v1.0.0, artic-chikv-ecsa/400/v1.0.0, artic-dezi-pan-denv/1000/v1.0.0, artic-flu-a/800/v1.0.0, artic-inrb-mpox/400/v1.0.0, artic-inrb-mpox/2500/v1.0.0, artic-inrb-mpox/2500/v1.0.0-cladeia, artic-inrb-mpox/2500/v1.0.0-cladeib and 60 more

primer_bed (file) required: Custom primer BED file. Required when scheme_mode is custom.

reference_fasta (file) required: Custom reference FASTA matching the primer BED reference sequence names. Required when scheme_mode is custom.

custom_scheme_name (str): Optional display name for a custom scheme in the generated run report.

nextclade_dataset (str): Optional Nextclade dataset name applied to all samples, for example sars-cov-2. To see the available supported viruses, dataset names and tag information go to https://clades.nextstrain.org. Leave blank to disable Nextclade.

nextclade_tag (str): Optional Nextclade dataset tag or version. Used only when nextclade_dataset is provided.

Links

Home page

Documentation

GitHub repository

License: MIT

Cite as: ARTIC Network. amplicon-nf: Amplicon genome assembly for ARTIC-style primer schemes using Nextflow. https://github.com/artic-network/amplicon-nf

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