{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T18:07:55Z","timestamp":1789063675707,"version":"build-2803163510"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["862874"],"award-info":[{"award-number":["862874"]}]},{"name":"European Union's Horizon Europe","award":["101136346"],"award-info":[{"award-number":["101136346"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    African Swine Fever Virus (ASFV) is of high concern in porcine livestock across the world due to both the high mortality rates and the trade restrictions imposed on affected regions. The viral genome is large and complex, and genomic analysis is essential for tracing its origin and evolution. Although several bioinformatics tools exist for genome assembly and analysis, no single platform integrates all necessary steps in an accessible and systematic way. In this study the authors developed \u2018PePApipe\u2019, a custom-built, user-friendly pipeline that enables rapid, complete, and efficient ASFV genome analysis. It is specifically designed for laboratory professionals with limited bioinformatics experience, requiring only basic command-line knowledge. Starting from raw sequencing data, PePApipe integrates thirteen software tools into one automated workflow, covering quality control and pre-processing of raw reads,\n                    <jats:italic>de novo<\/jats:italic>\n                    genome assembly and variant calling. Programmed in Python, it can be executed locally through bash scripts, or using a Slurm protocol for batch processing of multiple samples. The main outputs are the ASFV consensus genome sequence and a file listing its putative variants compared to the selected reference genome. PePApipe classifies generated files into structured folders and produces intermediate files that can be used as inputs for further or parallel analyses; users can also enable or disable specific steps in each particular case. This pipeline is adaptable and complementary to downstream steps such as viral genome annotation or genome visualization. By consolidating all stages of viral genome analysis into a single automated workflow, PePApipe reduces the likelihood of user error, and enhances reproducibility and efficiency. This user-friendly pipeline facilitates the transition from sequencing to assembly and downstream analysis of viral genomes, ensuring a fast and reliable response to molecular analysis demands. Finally, the pipeline can be easily adapted to the study of other viral species, expanding its application in infectious diseases surveillance.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0356006","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T17:28:36Z","timestamp":1789061316000},"page":"e0356006","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["\u2018PePApipe\u2019: A complete bioinformatics analysis pipeline for African Swine Fever Virus genome"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3558-9260","authenticated-orcid":true,"given":"Vicente","family":"Lopez-Chavarrias","sequence":"first","affiliation":[{"name":"Centro de Investigaci\u00f3n en Sanidad Animal (CISA), Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","place":["Valdeolmos, Madrid, Spain"],"department":["Department of Infectious Diseases and Global Health"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8059-034X","authenticated-orcid":true,"given":"Irene","family":"Aldea","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Sanidad Animal (CISA), Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","place":["Valdeolmos, Madrid, Spain"],"department":["Department of Infectious Diseases and Global Health"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9919-0112","authenticated-orcid":true,"given":"Jovita","family":"Fern\u00e1ndez-Pinero","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Sanidad Animal (CISA), Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","place":["Valdeolmos, Madrid, Spain"],"department":["Department of Infectious Diseases and Global Health"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"issue":"5","key":"pone.0356006.ref001","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1099\/jgv.0.001049","article-title":"ICTV virus taxonomy profile: Asfarviridae","volume":"99","author":"C Alonso","year":"2018","journal-title":"J Gen Virol"},{"key":"pone.0356006.ref002","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.vetmic.2016.10.003","article-title":"Challenges for African swine fever vaccine development-\"\u2026 perhaps the end of the beginning.\"","volume":"206","author":"DL Rock","year":"2017","journal-title":"Vet Microbiol"},{"key":"pone.0356006.ref003","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.tvjl.2017.12.025","article-title":"African swine fever: A re-emerging viral disease threatening the global pig industry","volume":"233","author":"PJ S\u00e1nchez-Cord\u00f3n","year":"2018","journal-title":"Vet J"},{"issue":"1","key":"pone.0356006.ref004","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.virusres.2012.10.030","article-title":"Epidemiology of African swine fever virus","volume":"173","author":"S Costard","year":"2013","journal-title":"Virus Res"},{"issue":"6","key":"pone.0356006.ref005","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1111\/tbed.12989","article-title":"Emergence of African Swine Fever in China, 2018","volume":"65","author":"X Zhou","year":"2018","journal-title":"Transbound Emerg Dis"},{"key":"pone.0356006.ref006","doi-asserted-by":"crossref","first-page":"197676","DOI":"10.1016\/j.virusres.2019.197676","article-title":"African swine fever (ASF) diagnosis, an essential tool in the epidemiological investigation","volume":"271","author":"C Gallardo","year":"2019","journal-title":"Virus Res"},{"issue":"1","key":"pone.0356006.ref007","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/s40249-018-0495-3","article-title":"African swine fever: an unprecedented disaster and challenge to China","volume":"7","author":"T Wang","year":"2018","journal-title":"Infect Dis Poverty"},{"issue":"1","key":"pone.0356006.ref008","doi-asserted-by":"crossref","first-page":"2146537","DOI":"10.1080\/22221751.2022.2146537","article-title":"African swine fever virus - 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