A Specialized Workflow for Bacterial Pathogenomics and Genomic Epidemiology
Microbe-Flow is an easy to setup, modular and flexible workflow for analyzing bacterial whole genome sequencing (WGS) data. It is based on the NeatSeq-Flow platform for modular workflows design and efficient execution on computer clusters. Microbe-Flow uses a wide range of tools to enable a comprehensive overview on large numbers of samples. Microbe-Flow offers an automated solution for WGS, starting from FASTQ files, including raw reads quality control (QC), de novo assembly and its QC, gene prediction and annotation including virulence/resistance genes, phylogenetic analyses and typing based on variant calling and core SNPs, multilocus sequence typing (MLST) and core genome (cg)MLST. Notably, Microbe-Flow enables a range of studies including pan-genome and association analysis for desired bacterial attributes, bi-clustering of virulence genes including enrichment and gene clusters co-localization tests. Conveniently, Microbe-Flow is not species-specific and can be adjusted to any bacterium, while species-specific steps can be added as needed. Additionally, Microbe-Flow produces a detailed final report. Microbe-Flow was designed to work hand in hand with CONDA environments to enable an easy installation of almost all the pre-required programs and packages. Finally, Microbe-Flow is well documented and has step by step walk through instructions.
Documentation and installation