PathoSeq-QC: a bioinformatic pipeline that allows robust analysis of next generation sequencing raw data associated to viruses.
Recommendations on the use of genomics for surveillance are evidence that high-throughput genomic sequencing is a key technology to fight global health threats like COVID-19 pandemic. Together with Bioinformatics and other data sources (e.g., epidemiological information), it is used to get knowledge on health pathogenic threats, insights on their evolution, to monitor pathogens spread and to evaluate the effectiveness of countermeasures at policymaking level.
From a decision-making policy perspective, quality checks on the whole procedure are fundamental before making any analysis and conclusion, especially in pandemic events, when there's urgent need to get correct results to formulate decisions.
Here we present PathoSeq-QC, a bioinformatic “decision-tree” workflow, developed for SARS-CoV-2 but customisable to any viral threat, aimed to assessing whether conclusions are substantiated by solid and high-quality inputs. As example, wrongly detected SARS-CoV-2 variants leads to incorrect lineages assignations. PathoSeq-QC helps in i.evaluating the quality of the raw data; ii. assessing whether the analysed sample is composed by single or multiple lineages; iii.understanding whether the produced data are in support of a recombinant virus, a novel or an already known lineage.
We expect PathoSeq-QC to contribute to pathogens surveillance protocols robustness through the definition of quality standard criteria to avoid wrong conclusions that might influence decision making.
LEONI Gabriele;
PETRILLO Mauro;
2024-06-03
Publications Office of the European Union
JRC135827
978-92-68-16698-7 (online),
OP KJ-09-24-369-EN-N (online),
https://publications.jrc.ec.europa.eu/repository/handle/JRC135827,
10.2760/316105 (online),
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