{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T19:17:17Z","timestamp":1777922237145,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T00:00:00Z","timestamp":1673568000000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Feilman and Stan Perron Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n SAMStat is an efficient program to extract quality control metrics from fastq and SAM\/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and mapping error profiles split by mapping quality. This allows users to rapidly identify reasons for poor mapping including the presence of untrimmed adapters or poor sequencing quality at individual read positions.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Here, we present a major update to SAMStat. The new version now supports paired-end and long-read data. Quality control plots are drawn using the ploty javascript library.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The source code of SAMStat and code to reproduce the results are found here: https:\/\/github.com\/timolassmann\/samstat.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad019","type":"journal-article","created":{"date-parts":[[2023,1,14]],"date-time":"2023-01-14T01:26:52Z","timestamp":1673659612000},"source":"Crossref","is-referenced-by-count":8,"title":["SAMStat 2: quality control for next generation sequencing data"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0138-2691","authenticated-orcid":false,"given":"Timo","family":"Lassmann","sequence":"first","affiliation":[{"name":"Precision Health, Telethon Kids Institute, University of Western Australia , Perth, WA 6009, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,1,13]]},"reference":[{"key":"2023011909443574000_btad019-B1","author":"Andrews","year":"2010"},{"key":"2023011909443574000_btad019-B2","doi-asserted-by":"crossref","first-page":"giab007","DOI":"10.1093\/gigascience\/giab007","article-title":"HTSlib: C library for reading\/writing high-throughput sequencing data","volume":"10","author":"Bonfield","year":"2021","journal-title":"GigaScience"},{"key":"2023011909443574000_btad019-B3","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2023011909443574000_btad019-B4","doi-asserted-by":"crossref","first-page":"3048","DOI":"10.1093\/bioinformatics\/btab135","article-title":"RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts","volume":"37","author":"Graubert","year":"2021","journal-title":"Bioinformatics"},{"key":"2023011909443574000_btad019-B5","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1093\/bioinformatics\/btq614","article-title":"SamStat: monitoring biases in next generation sequencing data","volume":"27","author":"Lassmann","year":"2011","journal-title":"Bioinformatics"},{"key":"2023011909443574000_btad019-B6","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res"},{"key":"2023011909443574000_btad019-B7","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":"2023011909443574000_btad019-B8","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"The ENCODE Project Consortium","year":"2012","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad019\/48691572\/btad019.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btad019\/48769994\/btad019.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btad019\/48769994\/btad019.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T09:55:02Z","timestamp":1674122102000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad019\/6986964"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":8,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad019","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"btad019"}}