Chukamnerd Arnon, Jeenkeawpiam Kongpop, Chusri Sarunyou, Pomwised Rattanaruji, Singkhamanan Kamonnut, Surachat Komwit
Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand.
Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand.
Microorganisms. 2023 Jul 6;11(7):1769. doi: 10.3390/microorganisms11071769.
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.
细菌病原体的全基因组测序（WGS）在微生物学、医学和临床研究中广泛开展，以探索可能影响临床治疗和分子流行病学的遗传学见解。然而，分析细菌的WGS数据对微生物学家、临床医生和研究人员来说可能具有挑战性，因为这需要应用多个生物信息学流程从原始数据中提取遗传信息。在本文中，我们介绍了BacSeq，这是一种用于分析细菌基因组下一代测序数据的自动化生物信息学流程。BacSeq能够对负责多重耐药性、毒力因子和质粒的关键基因进行组装、注释和鉴定。此外，该流程整合了分离株之间的比较分析，提供系统发育树分析和单核苷酸多态性（SNP）鉴定。为便于在单个步骤中轻松分析并支持多个分离株的处理，BacSeq提供了基于JAVA平台的图形用户界面（GUI）。它旨在满足没有广泛生物信息学技能的用户的需求。
