Nextclade

Introduction

Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.

For more information, please check its | Docker hub: https://hub.docker.com/r/nextstrain/nextclade and its home page: https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli.html.

Versions

• 1.10.3

Commands

• nextclade

Module

You can load the modules by:

module load biocontainers
module load nextclade

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Nextclade on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nextclade
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers nextclade

mkdir -p data
nextclade dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2'

nextclade \
    --in-order \
    --input-fasta data/sars-cov-2/sequences.fasta \
    --input-dataset data/sars-cov-2 \
    --output-tsv output/nextclade.tsv \
    --output-tree output/nextclade.auspice.json \
    --output-dir output/ \
    --output-basename nextclade