• Script overview
• Usage
  • Prepare environment
  • How to run:
  • Output
• Program versions

This is written specifically for the venom group at UiO and is integrated with the supercomputer Saga at Sigma2.

This Snakemake pipeline takes a file of peptides/proteins and produces a summary table that can be used for toxin annotation. Specifically, it:

• Runs CD-HIT to cluster sequences with 100% similarity to remove redundancy.
• Annotates signal peptides using SignalP5.
• Annotates sequences that have signal peptides with:
  • InterProScan
  • Tox-Prot (with an e-value of 1e-3), producing a multi-FASTA file for each hit.
• Groups sequences using psiblast (e-value: 1e-3, inclusion_ethresh: 1e-10, and 3 iterations) and then uses an Union-Find algorithm to cluster groups with shared hits. Each group then gets its own number ID.
• Executes a summary script which creates the output table, with the columns:

No installation required, everything you need is already prepared. Before using the script, make sure the required environment is set up.

First, set up a tmux or screen environment (to run the pipeline while offline), then run:

module load Mamba/4.14.0-0
source ${EBROOTMAMBA}/bin/activate
conda activate /cluster/projects/nn9825k/admin/mamba/marius_snakemake

python master.py --account ACCOUNT --fasta FASTA

usage: master.py [-h] --account ACCOUNT --fasta FASTA

Run snakemake pipeline

options:
  -h, --help         show this help message and exit
  --account ACCOUNT  Input slurm account
  --fasta FASTA      Path to the input FASTA file

.
├── 0_slurm_logs
├── 1_SignalP5
├── 2_toxprot_hits_and_alignments <-- TOX-PROT MULTI-FASTA's
├── 3_interproscan
├── 4_toxin_groups
├── CD1_SP_Your_File_summary.tsv <-- OUTPUT TABLE
├── master.py
├── README.md
├── slurm_scripts
├── snakefiles
├── tmp
└── toxprot

• SignalP v5.0
• CD-HIT v4.8.1
• SeqKit v2.3.1
• InterProScan v5.62-94.0
• parallel v20220722
• BLAST+ v2.13.0
• BLAST+/2.14.0-gompi-2022b (group toxins)
• Biopython/1.81-foss-2022b (group toxins)