| Title: |
SPARKI: a tool for the statistical analysis of pathogen identification results |
| Authors: |
Boccacino, Jacqueline M; del Castillo Velasco-Herrera, Martin; Beale, Mathew A; Billington, Jamie; Vermes, Ian; Obolenski, Sofia; Wong, Kim; Torrens, Laura; Moody, Sarah; Perdomo, Sandra; Cheema, Saamin; Francis, Bailey; Offord, Victoria; Butler, Adam P; Adams, David J |
| Contributors: |
Kendziorski, Christina; Medical Research Council; Wellcome Trust |
| Source: |
Bioinformatics ; volume 41, issue 11 ; ISSN 1367-4803 1367-4811 |
| Publisher Information: |
Oxford University Press (OUP) |
| Publication Year: |
2025 |
| Description: |
Motivation Many pathogen identification and microbiome analysis tools have been developed in recent years, with Kraken 2 being one of the most popular. While tools downstream of Kraken 2 can assist in the interpretation of its outputs, a statistical framework to assess the likelihood that a taxon/organism is present in a single sample alongside an automated end-to-end analysis pipeline has not yet been fully implemented. Results Here, we introduce SPARKI, an R package that performs statistical analysis of Kraken 2 outputs and aids in the identification of pathogens present in next-generation sequencing samples. SPARKI adds to the field by bringing a probabilistic view to Kraken 2 data, serving as a discovery tool and complementing other methods such as KrakenTools, Bracken, and Pavian. Availability and implementation SPARKI code is available on GitHub at https://github.com/team113sanger/sparki. SPARKI is also part of an end-to-end pathogen identification pipeline, sparki-nf, which is available at https://github.com/team113sanger/sparki-nf. An additional pipeline for further exploration and validation of SPARKI results is also available at https://github.com/team113sanger/map-to-genome. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1093/bioinformatics/btaf596 |
| DOI: |
10.1093/bioinformatics/btaf596/65044847/btaf596.pdf |
| Availability: |
https://doi.org/10.1093/bioinformatics/btaf596; https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf596/65044847/btaf596.pdf; https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf596/65044847/btaf596.pdf |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.B821A9EE |
| Database: |
BASE |