{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T07:18:32Z","timestamp":1775027912261,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,22]],"date-time":"2022-08-22T00:00:00Z","timestamp":1661126400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>The FASTQ+ format is designed for single-cell experiments. It extends various optional tags, including cell barcodes and unique molecular identifiers, to the sequence identifier and is fully compatible with the FASTQ format. In addition, PISA implements various utilities for processing sequences in the FASTQ format and alignments in the SAM\/BAM\/CRAM format from single-cell experiments, such as converting FASTQ format to FASTQ+, annotating alignments, PCR deduplication, feature counting and barcodes correction. The software is open-source and written in C language.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/doi.org\/10.5281\/zenodo.7007056 or https:\/\/github.com\/shiquan\/PISA<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac562","type":"journal-article","created":{"date-parts":[[2022,8,22]],"date-time":"2022-08-22T13:57:48Z","timestamp":1661176668000},"page":"4639-4642","source":"Crossref","is-referenced-by-count":46,"title":["The FASTQ+ format and PISA"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3681-1353","authenticated-orcid":false,"given":"Quan","family":"Shi","sequence":"first","affiliation":[{"name":"BGI-Shenzhen , Shenzhen 518103, China"},{"name":"Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen , Copenhagen 2100, Denmark"}]},{"given":"Shiping","family":"Liu","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen , Shenzhen 518103, China"}]},{"given":"Karsten","family":"Kristiansen","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen , Shenzhen 518103, China"},{"name":"Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen , Copenhagen 2100, Denmark"},{"name":"Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences , BGI-Qingdao, Qingdao 166555, P. R. China"}]},{"given":"Longqi","family":"Liu","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen , Shenzhen 518103, China"}]}],"member":"286","published-online":{"date-parts":[[2022,8,22]]},"reference":[{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1146\/annurev-genom-091416-035324","article-title":"Single-cell (multi) omics technologies","volume":"19","author":"Chappell","year":"2018","journal-title":"Annu. Rev. Genomics Hum. Genet"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023041408233368300_","first-page":"1","article-title":"Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE","volume":"12","author":"He","year":"2021","journal-title":"Nat. Commun"},{"key":"2023041408233368300_","author":"Kaminow","year":"2021"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res"},{"key":"2023041408233368300_","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac562\/45509863\/btac562.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4639\/49884724\/btac562.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4639\/49884724\/btac562.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T01:17:37Z","timestamp":1700961457000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/19\/4639\/6673134"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,8,22]]},"references-count":9,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2022,9,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac562","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,10,1]]},"published":{"date-parts":[[2022,8,22]]}}}