SID-Chart

An automatic pipeline for the BGC characterization of genomes. Moreover, it should integrate further data layers, such as a phylogenetic tree and the similarity to specific proteins.

Prerequisites

• Nextflow installed
• Docker installed
• Docker images for:
  • antiSMASH
  • MMseqs2
  • BiG-SCAPE
  • chewBBACA
  • MEGA-CC
• Streamlit installed
• pandas installed
• seaborn installed
• matplotlib installed
• Java 17 or later
• Pyhton 3.0

Input

SID-Chart expects input data in the following format.

└── Data
    ├── dataset_staphy
        ├── ncbi_dataset
            ├── GCA_000433035.1
                ├── GCA_000433035.1_MGS324_genomic.fna
                ├── genomic.gbff
                └── protein.faa
            ├── ...
            └── ...
    ├── reference_BGCs
        ├── BGC0000943.gbk
        ├── ...
        └── ...
    ├── reference_genome
        └── GCF_001027105.1_ASM102710v1_genomic.fna
    ├── metadata.tsv
    ├── overviewBGCs.csv
    ├── proteins_uptake.fa
    └── Staphylococcus_aureus.trn

• ncbi_dataset/ — Contains information about all species to be analyzed.
• reference_BGCs/ — Contains all biosynthetic gene clusters (BGCs) to be included in the analysis.
• reference_genome/ — Contains a FASTA file of a reference species required by chewBBACA.
• metadata.tsv — Lists the accession numbers and corresponding NCBI organism names.
• overviewBGC.csv — Provides a mapping between BGCs and lipoproteins.
• proteins_uptake.fa — Contains the lipoproteins to be analyzed.
• Staphylococcus_aureus.trn — A Prodigal training file required by chewBBACA (can be created using Pyrodigal)

File and folder naming expected by SID-Chart can be customized via nextflow.conf.

Run Pipeline

• Check that the input file names correspond to the default parameters defined in nextflow.conf.
• If they differ, either modify the values in nextflow.conf or provide the correct file names as arguments in run_pipeline.sh.
• Set the input directory inside the run_pipeline.sh script by defining it as the --input parameter in the Nextflow command.
• Inside the nf directory run:

./run_pipeline.sh [RUN_NAME]

Run Visualization

• Inside the web directory run:

./run_visualization.sh [RUN_NAME]