{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T08:02:59Z","timestamp":1774944179284,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,12]],"date-time":"2021-11-12T00:00:00Z","timestamp":1636675200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"CNIO Bioinformatics Unit was supported by the Instituto de Salud Carlos III","award":["RTI2018-097596-B-I00"],"award-info":[{"award-number":["RTI2018-097596-B-I00"]}]},{"name":"AEI-MCIU and ERDF-EU"},{"name":"Spanish National Bioinformatics Institute (ELIXIR-ES, INB","award":["PT17\/0009\/0011-ISCIII-SGEFI\/ERDF"],"award-info":[{"award-number":["PT17\/0009\/0011-ISCIII-SGEFI\/ERDF"]}]},{"DOI":"10.13039\/100012818","name":"Comunidad de Madrid","doi-asserted-by":"publisher","award":["S2017\/ 65 BMD-3778"],"award-info":[{"award-number":["S2017\/ 65 BMD-3778"]}],"id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Structural and Investment Fund"},{"DOI":"10.13039\/100016778","name":"Paradifference Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016778","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>bollito is an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data. Starting from FASTQ files or preprocessed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis integrating &amp;gt;30 state-of-the-art tools. This includes quality control, read alignment, dimensionality reduction, clustering, cell-marker detection, differential expression, functional analysis, trajectory inference and RNA velocity. bollito is built using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results. bollito\u2019s modular design makes it easy to incorporate other packages into the pipeline enabling its expansion with new functionalities.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code is freely available at https:\/\/gitlab.com\/bu_cnio\/bollito under the MIT license.<\/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\/btab758","type":"journal-article","created":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T20:18:03Z","timestamp":1636489083000},"page":"1155-1156","source":"Crossref","is-referenced-by-count":13,"title":["bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses"],"prefix":"10.1093","volume":"38","author":[{"given":"Luis","family":"Garc\u00eda-Jimeno","sequence":"first","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Coral","family":"Fustero-Torre","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda Jos\u00e9","family":"Jim\u00e9nez-Santos","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4146-0551","authenticated-orcid":false,"given":"Gonzalo","family":"G\u00f3mez-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom\u00e1s","family":"Di Domenico","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2373-769X","authenticated-orcid":false,"given":"F\u00e1tima","family":"Al-Shahrour","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO) , Madrid 28029, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,12]]},"reference":[{"key":"2023020108515484000_btab758-B1","doi-asserted-by":"crossref","first-page":"4376","DOI":"10.1038\/s41467-019-12235-0","article-title":"Functional interpretation of single cell similarity maps","volume":"10","author":"DeTomaso","year":"2019","journal-title":"Nat. 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