BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes

Abstract

Whole-genome sequencing (WGS) of bacterial pathogens is widely conducted in microbiological, medical, and clinical research to explore genetic insights that could impact clinical treatment and molecular epidemiology. However, analyzing WGS data of bacteria can pose challenges for microbiologists, clinicians, and researchers, as it requires the application of several bioinformatics pipelines to extract genetic information from raw data. In this paper, we present BacSeq, an automated bioinformatic pipeline for the analysis of next-generation sequencing data of bacterial genomes. BacSeq enables the assembly, annotation, and identification of crucial genes responsible for multidrug resistance, virulence factors, and plasmids. Additionally, the pipeline integrates comparative analysis among isolates, offering phylogenetic tree analysis and identification of single-nucleotide polymorphisms (SNPs). To facilitate easy analysis in a single step and support the processing of multiple isolates, BacSeq provides a graphical user interface (GUI) based on the JAVA platform. It is designed to cater to users without extensive bioinformatics skills.

Unlocking the genetic potential of Lacticaseibacillus rhamnosus strains: Medical applications of a promising probiotic for human and animal health

“…One gigabase pair of 150 bp paired-end reads per sample was generated from the sequencer in FASTQ format. We then used the automated bioinformatics pipeline, Bacseq v1.0.0 [ 14 ], to analyze raw sequence data. This tool is capable of performing de novo assembly and annotation of genes, tRNA, and rRNA in bacterial genomes using SPAdes v3.15.5 [ 15 ], Prokka v1.12 [ 16 ], tRNAscan-SE [ 17 ] and RNAmmer [ 18 ], respectively.…”

Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand

“…The BacSeq pipeline [17], a bioinformatic tool designed for analyzing bacterial genomes, was used for de novo assembly, quality assessment, genome annotation, and evaluation of genome completeness. Antimicrobial resistance genes were identified using ABRicate version 1.0.1 [18] against the comprehensive antibiotic resistance database (CARD) [19].…”

Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot

“…The WGS workflow contains four basic steps: nucleic acid (NA) extraction, library preparation (LP), sequencing, and data analysis. LP represents one of the most labor-intensive step of the whole workflow, as sequencing is performed on automated NGS-platforms and subsequent data analyses often is using automated bioinformatic pipelines 10 – 12 . NA extraction can either be performed on fully automated NA-extraction platforms or manually, depending on the sample type and microbial species under investigation 12 .…”