Sumario: |
ASGARD+ (Accelerated Sequential Genome-analysis and Antibiotic Re-
sistance Detection) is a command-line platform for automatic identification
of antibiotic-resistance genes in bacterial genomes, providing an easy-to-use
interface to process big batches of sequence files from whole genome se-
quencing, with minimal configuration. It also provides a CPU-optimization
algorithm that reduces the processing time. This tool consists of two main pro-
tocols. The first one, ASGARD, is based on the identification and annotation of
antimicrobial resistance elements directly from the short reads using different
public databases. SAGA, enables the alignment, indexing, and mapping of
whole-genome samples against a reference genome for the detection and call
of variants, as well as the visualization of the results through the construction
of a tree of SNPs. The application of both protocols is performed using just
one short command and one configuration file based on JSON syntax, which
modulates each pipeline step, allowing the user to do as many interventions
as needed on the different software tools that are adapted to the pipeline. The
modular ASGARD+ allows researchers with little experience in bioinfor-
matic analysis and command-line use to quickly explore bacterial genomes in
depth, optimizing analysis times and obtaining accurate results. © 2023 Wiley
Periodicals LLC.
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