{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T04:29:23Z","timestamp":1783571363923,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T00:00:00Z","timestamp":1626912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Union\u2019s H2020 research and innovation programme under Marie Sklodowska-Curie","award":["754422"],"award-info":[{"award-number":["754422"]}]},{"name":"Spanish Ministry of Economy, Industry and Competitiveness","award":["PGC2018-098152-A-100"],"award-info":[{"award-number":["PGC2018-098152-A-100"]}]},{"name":"Spanish Ministry of Science and Innovation to the EMBL partnership"},{"name":"Centro de Excelencia Severo Ochoa and CERCA Programme\/Generalitat de Catalunya"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ModPhred is available at https:\/\/github.com\/novoalab\/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab539","type":"journal-article","created":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T07:34:08Z","timestamp":1626852848000},"page":"257-260","source":"Crossref","is-referenced-by-count":18,"title":["ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0790-067X","authenticated-orcid":false,"given":"Leszek P","family":"Pryszcz","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"},{"name":"International Institute of Molecular and Cell Biology , 02-109 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9367-6311","authenticated-orcid":false,"given":"Eva Maria","family":"Novoa","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,22]]},"reference":[{"key":"2023020108391952700_btab539-B1","doi-asserted-by":"crossref","DOI":"10.1038\/s41587-021-00915-6","article-title":"Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing","author":"Begik","year":"2021","journal-title":"Nat. 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