{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T02:59:01Z","timestamp":1775789941209,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,12,6]],"date-time":"2018-12-06T00:00:00Z","timestamp":1544054400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U41HG007497"],"award-info":[{"award-number":["U41HG007497"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Harmonizing quality control (QC) of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample QC metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard QC metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. The versatility of Alfred allows for easy pipeline integration in high-throughput settings, including DNA sequencing facilities and large-scale research initiatives, enabling continuous monitoring of sequence data quality and characteristics across samples. Alfred supports haplo-tagging of BAM\/CRAM files to conduct haplotype-resolved analyses in conjunction with a variety of next-generation sequencing based assays. Alfred\u2019s companion web application enables interactive exploration of results and comparison to public datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Alfred is open-source and freely available at https:\/\/tobiasrausch.com\/alfred\/.<\/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\/bty1007","type":"journal-article","created":{"date-parts":[[2018,12,5]],"date-time":"2018-12-05T20:13:02Z","timestamp":1544040782000},"page":"2489-2491","source":"Crossref","is-referenced-by-count":87,"title":["Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5773-5620","authenticated-orcid":false,"given":"Tobias","family":"Rausch","sequence":"first","affiliation":[{"name":"Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany"},{"name":"Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany"}]},{"given":"Markus","family":"Hsi-Yang Fritz","sequence":"additional","affiliation":[{"name":"Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany"}]},{"given":"Jan O","family":"Korbel","sequence":"additional","affiliation":[{"name":"Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany"}]},{"given":"Vladimir","family":"Benes","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,12,6]]},"reference":[{"key":"2023062712221165600_bty1007-B1","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/bioinformatics\/bts196","article-title":"RNA-SeQC: RNA-seq metrics for quality control and process optimization","volume":"28","author":"DeLuca","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062712221165600_bty1007-B2","doi-asserted-by":"crossref","first-page":"R98.","DOI":"10.1186\/gb-2012-13-10-r98","article-title":"CHANCE: comprehensive software for quality control and validation of ChIP-seq data","volume":"13","author":"Diaz","year":"2012","journal-title":"Genome Biol"},{"key":"2023062712221165600_bty1007-B3","first-page":"2","article-title":"Standardization and quality management in next-generation sequencing","volume":"10","author":"Endrullat","year":"2016","journal-title":"Appl. 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