Publication
ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents
| dc.contributor.author | Cruz, Helena | |
| dc.contributor.author | Pinheiro, Miguel | |
| dc.contributor.author | Borges, Vítor | |
| dc.date.accessioned | 2025-03-20T11:11:25Z | |
| dc.date.available | 2025-03-20T11:11:25Z | |
| dc.date.issued | 2024-03-09 | |
| dc.description | This article belongs to the Special Issue Machine Learning Applications in Bioinformatics and Biomedicine. | |
| dc.description.abstract | In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like and . In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub. | |
| dc.description.sponsorship | V.B. work on ReporType development was co-financed through the DURABLE project. The DURABLE project has been co-funded by the European Union, under the EU4Health Programme (EU4H), Project no. 101102733. This work was also partially funded by the European Union through the project “Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal” on behalf of EU4H programme (EU4H-2022-DGA-MS-IBA-1). | |
| dc.identifier.citation | Int J Mol Sci. 2024 Mar 9;25(6):3172. doi: 10.3390/ijms25063172 | |
| dc.identifier.issn | 1661-6596 | |
| dc.identifier.pmid | 38542144 | |
| dc.identifier.uri | http://hdl.handle.net/10400.18/10445 | |
| dc.language.iso | eng | |
| dc.peerreviewed | yes | |
| dc.publisher | MDPI | |
| dc.relation | 101102733 | |
| dc.relation | EU4H-2022-DGA-MS-IBA-1 | |
| dc.relation.hasversion | https://www.mdpi.com/1422-0067/25/6/3172 | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| dc.subject | Bioinformatics | |
| dc.subject | Genotyping | |
| dc.subject | Loci Screening | |
| dc.subject | Pathogen | |
| dc.subject | Sequencing | |
| dc.title | ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents | por |
| dc.type | research article | |
| dspace.entity.type | Publication | |
| oaire.citation.issue | 6 | |
| oaire.citation.startPage | 3172 | |
| oaire.citation.title | International Journal of Molecular Sciences | |
| oaire.citation.volume | 25 | |
| oaire.version | http://purl.org/coar/version/c_970fb48d4fbd8a85 |