5 Genomic Characterization of Strains
Because WGS by definition captures the entirety of an organism’s
genome, it allows the characterization of much of the organism’s
underlying biology. This can include taxonomic identification as
described in the previous section, detailed phylogenetic or phylogenomic placement, functional annotation of genes, proteomic
analysis, antimicrobial resistance (AMR) gene detection, identification and annotation of sequence variations, molecular epidemiology, and much more.
This section describes various tools that can be used generally
for characterization of bacterial strains using genomic features as
well as some tools specific to characterization of mycobacteria.
5.1 The
Pathosystems
Resource Integration
Center (PATRIC)
The Bioinformatics Resource Center (BRC) program was established by the National Institute of Allergy and Infectious Diseases
(NIAID) in 2004. Its primary focus is on providing access to
genome sequence data and analysis tools for studying pathogens.
The PathoSystems Resource Integration Center (PATRIC) began
as one of the original centers tasked with supporting comparative
analysis of bacterial pathogens [105–107]. Over the years, the
PATRIC resource has expanded and adapted to keep pace with
the growth in bioinformatic datasets and the need for associated
analysis tools. This includes providing a number of bioinformatic
services that are designed to enable easy access to complex bioinformatic workflows, which can be accessed via the PATRIC web
interface or a command line interface. The first services, which
allowed users to assemble and annotate genomes, were launched
in January 2015. These services have expanded to provide a
one-shop, comprehensive analysis resource for researchers with
bacterial genome sequences. In 5 years, just under 300,000 jobs
have been submitted to the different PATRIC services. Different
bioinformatic services are described below, with their order following a potential analysis strategy for analyzing sequence reads or
contigs.
5.1.1 FASTQ Utilities
Understanding the quality of reads that come from a sequencer is
an essential first step to any analysis that uses them. The FASTQ
Utilities Service enables users to align reads, measure base call
quality, and trim low-quality sequences from read files. The service
accepts long- or short-read files in single or paired-end format. It
can also retrieve read files directly from the NCBI Sequence Read
Archive (SRA). The service has three components, ‘trim,’
‘FastQC,’ and ‘align,’ which can be used independently or in any
combination. The trimming component, an essential first task prior
to analysis, finds and removes adaptors from reads and uses Trim
Galore [108]. The FastQC [30] component provides quality
434
Marco A. Riojas et al.
Because WGS by definition captures the entirety of an organism’s
genome, it allows the characterization of much of the organism’s
underlying biology. This can include taxonomic identification as
described in the previous section, detailed phylogenetic or phylogenomic placement, functional annotation of genes, proteomic
analysis, antimicrobial resistance (AMR) gene detection, identification and annotation of sequence variations, molecular epidemiology, and much more.
This section describes various tools that can be used generally
for characterization of bacterial strains using genomic features as
well as some tools specific to characterization of mycobacteria.
5.1 The
Pathosystems
Resource Integration
Center (PATRIC)
The Bioinformatics Resource Center (BRC) program was established by the National Institute of Allergy and Infectious Diseases
(NIAID) in 2004. Its primary focus is on providing access to
genome sequence data and analysis tools for studying pathogens.
The PathoSystems Resource Integration Center (PATRIC) began
as one of the original centers tasked with supporting comparative
analysis of bacterial pathogens [105–107]. Over the years, the
PATRIC resource has expanded and adapted to keep pace with
the growth in bioinformatic datasets and the need for associated
analysis tools. This includes providing a number of bioinformatic
services that are designed to enable easy access to complex bioinformatic workflows, which can be accessed via the PATRIC web
interface or a command line interface. The first services, which
allowed users to assemble and annotate genomes, were launched
in January 2015. These services have expanded to provide a
one-shop, comprehensive analysis resource for researchers with
bacterial genome sequences. In 5 years, just under 300,000 jobs
have been submitted to the different PATRIC services. Different
bioinformatic services are described below, with their order following a potential analysis strategy for analyzing sequence reads or
contigs.
5.1.1 FASTQ Utilities
Understanding the quality of reads that come from a sequencer is
an essential first step to any analysis that uses them. The FASTQ
Utilities Service enables users to align reads, measure base call
quality, and trim low-quality sequences from read files. The service
accepts long- or short-read files in single or paired-end format. It
can also retrieve read files directly from the NCBI Sequence Read
Archive (SRA). The service has three components, ‘trim,’
‘FastQC,’ and ‘align,’ which can be used independently or in any
combination. The trimming component, an essential first task prior
to analysis, finds and removes adaptors from reads and uses Trim
Galore [108]. The FastQC [30] component provides quality
434
Marco A. Riojas et al.