SARS-CoV-2 phylogenetic analysis pipeline.

CFIA-NCFAD/scovtree is a bioinformatics pipeline for SARS-CoV-2 phylogenetic analysis. Given an input FASTA file with SARS-CoV-2 sequences, this workflow will generate a maximum-likelihood phylogenetic tree (using IQ-TREE from a MAFFT or Nextalign multiple sequence alignment) and interactive HTML tree visualization (shiptv).

This pipeline also allows you to visualize your sequences along with the most closely SARS-CoV-2 sequences from GISAID (if both the GISAID sequences and metadata .tar.xz files are provided). Amino acid mutations can also be determined using Nextclade and shown in the tree visualization.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

1. Install nextflow

2. Install any of Docker, Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run CFIA-NCFAD/scovtree -profile test,<docker/singularity/conda>

4. Start running your own analysis!

   • Typical command for phylogenetic analysis:

     nextflow run CFIA-NCFAD/scovtree -profile <docker/singularity/conda> \
         --input your-sars-cov-2-sequences.fasta

   • Typical command for phylogenetic analysis with GISAID SARS-CoV-2 data:

     nextflow run CFIA-NCFAD/scovtree -profile <docker/singularity/conda> \
         --input your-sars-cov-2-sequences.fasta \
         --input_metadata your-sars-cov-2-sequences-metadata.tsv \
         --gisaid_sequences sequences_fasta_2021_12_01.tar.xz \
         --gisaid_metadata metadata_tsv_2021_12_01.tar.xz

CFIA-NCFAD/scovtree was originally written by Hai Nguyen.

Contributors:

• Peter Kruczkiewicz for workflow conceptualization and software development.
• jts/ncov-tools for bin/align2alleles.py and bin/phylogenetic_tree_snps.r to create phylogenetic tree with SNPs highlighted using R ggtree

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #scovtree channel (you can join with this invite).

This pipeline tries to follow the best practices for Nextflow workflow development and deployment set by nf-core. You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

In addition, references of tools and data used in this pipeline are as follows:

• nf-core
• jts/ncov-tools
• IQ-TREE
• Nextalign
• Nextclade
• MAFFT
• shiptv
• Pangolin
• ggtree
• GISAID
• SARS-CoV-2

Copyright 2021 Canadian Food Inspection Agency of Canada, Government of Canada.

Distributed under the MIT license.