BIP: a validated high-throughput sequencing test for the identification of bacteria

Bacterial identification methods like PCR and MALDI-TOF MS face limitations due to their targeted nature and database constraints. To overcome these limitations, we developed the Bacterial Identification Pipeline (BIP), an automated, untargeted test using Illumina sequencing. BIP utilizes a Snakemake workflow for automated quality control, de novo assembly, and annotation. It identifies species via the Genome Taxonomy Database and NCBI taxonomy check and provides context by generating phylogenetic trees based on average nucleotide identity (ANI). Ultimately, BIP offers a comprehensive, user-friendly, and high-resolution solution for the identification of bacteria, regardless of prior knowledge.