snphylo
Link to section 'Introduction' of 'snphylo' Introduction
Snphylo is a pipeline to generate a phylogenetic tree from huge SNP data.
Docker hub: https://hub.docker.com/r/finchnsnps/snphylo
Home page: https://github.com/thlee/SNPhylo
Link to section 'Versions' of 'snphylo' Versions
- 20180901
Link to section 'Commands' of 'snphylo' Commands
- Rscript
- snphylo.sh
- convert_fasta_to_phylip.py
- convert_simple_to_hapmap.py
- determine_bs_tree.R
- draw_unrooted_tree.R
- generate_snp_sequence.R
- remove_low_depth_genotype_data.py
- remove_no_genotype_data.py
Link to section 'Module' of 'snphylo' Module
You can load the modules by:
module load biocontainers
module load snphylo
Link to section 'Example job' of 'snphylo' 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 snphylo on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=snphylo
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snphylo