BADASS

BADASS analyzes bacteriocin sequences in whole-metagenome shotgun (WMS) datasets to identify, quantify, and characterize bacteriocin diversity for metagenomic discovery and ecological studies.

Key Features:

• Comprehensive pipeline: Performs a pipeline starting from quality assessment of raw WMS sequencing data.
• Sequence search and annotation: Searches for bacteriocin sequences using BLAST or DIAMOND against the BAGEL4 database.
• Abundance and richness calculation: Calculates bacteriocin abundance by comparing reads classified as bacteriocins to 16S rRNA gene reads using the SILVA database and assesses richness across three bacteriocin classes.
• Output generation: Produces plots and tabular files summarizing the richness and abundance of detected bacteriocins.

Scientific Applications:

• Bacteriocin prospecting in metagenomes: Identification and cataloging of putative bacteriocin sequences from WMS datasets for discovery studies.
• Microbial ecology and antimicrobial resistance studies: Quantification and distribution analyses of bacteriocin classes to support studies in microbial community function and antimicrobial dynamics.
• Demonstrative analysis: Application to four WMS datasets revealed lantibiotics as the most abundant bacteriocin class, commonly produced by Streptomyces.

Methodology:

Processes WMS raw reads with quality assessment, searches sequences using BLAST or DIAMOND against BAGEL4, compares bacteriocin-classified reads to 16S rRNA reads using SILVA to calculate abundance and richness across three bacteriocin classes, and outputs plots and tables.