nextclade
Link to section 'Introduction' of '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.
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.
Link to section 'Versions' of 'nextclade' Versions
- 1.10.3
Link to section 'Commands' of 'nextclade' Commands
- nextclade
Link to section 'Module' of 'nextclade' Module
You can load the modules by:
module load biocontainers
module load nextclade
Link to section 'Example job' of 'nextclade' Example job
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