BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes.
Arnon ChukamnerdKongpop JeenkeawpiamSarunyou ChusriRattanaruji PomwisedKamonnut SingkhamananKomwit SurachatPublished in: Microorganisms (2023)
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.
Keyphrases
- genome wide
- electronic health record
- escherichia coli
- big data
- copy number
- bioinformatics analysis
- high throughput
- healthcare
- palliative care
- pseudomonas aeruginosa
- staphylococcus aureus
- machine learning
- oxidative stress
- data analysis
- gene expression
- antimicrobial resistance
- dna methylation
- deep learning
- transcription factor
- biofilm formation
- multidrug resistant
- gram negative
- anti inflammatory
- cystic fibrosis
- candida albicans
- low cost
- genome wide identification