Bioprospecting

This repository contains the bioinformatic tools and custom code dedicated to the bioprospecting of Biosynthetic Gene Clusters (BGCs) in marine metagenomic samples.

The tools included are containerized, and have to be executed utilizing their corresponding run_* script.

Fig. 1. The input data consists of assembled metagenomics samples (fasta files) and their associated coverage estimates (bam files) previously generated with VEBA. The pipeline is organized in six main tasks. 1) Identify BGC sequences: the BGCs are annotated in the assembled metagenomic data utilizing antiSMASH and deepBGC. 2) Dereplicate BGC sequences: given that we are using two different tools to annotate BGCs, it is likely that some of the identified sequences will coincide (at least partially); in such cases, the longest BGC sequence is kept. 3) Taxonomic annotation: the metagenomic contigs containing BGC sequences are taxonomically annotated utilizing MMseqs taxonomy and the reference database UniRef100. 4) BGC mapping: the metagenomic BGC sequences are mapped against (previously constructed) Gene Cluster Family (GCF) models of the database MIBiG v3 utilizing BiG-SLICE; 5) BGC clustering: the metagenomic BGC sequences are clustered into GCFs with BiG-SLICE; 6) Compute coverage: the coverage of the metagenomic contigs, previously estimated with VEBA, is utilized to determine the coverage of the BGC sequences. The output of the pipeline consists of the following tables: Table 1: functional and taxonomic annotation, biosynthetic novelty, and closest GCF id; Table 2: GCF abundance table; Table 3: BGC class abundance table.

Repository structure

.
├── execution
│   ├── bgc_annotation
│   │   ├── antismash_execution.ipynb
│   │   └── src
│   │       ├── antismash_Dockerfile
│   │       ├── requirements.txt
│   │       ├── run_antismash.sh
│   │       └── utilitites.ipynb
│   ├── bgc_clustering
│   │   ├── bigslice_execution.ipynb
│   │   └── src
│   │       ├── bigslice_Dockerfile
│   │       ├── requirements.txt
│   │       ├── run_bigslice.sh
│   │       └── utilitites.ipynb
│   ├── bgc_mapping
│   │   ├── bigslice_execution.ipynb
│   │   └── src
│   │       ├── bigslice_Dockerfile
│   │       ├── requirements.txt
│   │       ├── run_bigslice.sh
│   │       └── utilities.ipynb
│   └── bgc_taxonomy
│       ├── mmseqs_execution.ipynb
│       └── src
│           ├── mmseqs_Dockerfile
│           ├── requirements.txt
│           ├── run_mmseqs_taxonomy.sh
│           └── utilities.ipynb
├── figures
│   └── Bioprospectig_pipeline_dev.png
└── README.md

The execution folder contains all the modules that compose the bioprospecting pipeline. These are: bgc_annotation, bgc_clustering, bgc_mapping, and bgc_taxonomy.
Each of these modules consist of a folder with the following files:
The *_execution.ipynb NB: which contains the code and documentation necessary to run the analysis.
The src folder with the following files:

• *_Dockerfile to create the container to run the main tool(s) to be executed in a module.
• requirements.txt a list of all the packages needed to run the *_execution.ipynb NB.
• utilities.ipynb the definition of all the functions to be utilized in the *_execution.ipynb NB.
• run_*.sh a wrap script to easily execute the containerized tool(s).
  The figures folder contains the figures to be included in this repository as part of its documentation.