{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:30:13Z","timestamp":1772166613728,"version":"3.50.1"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T00:00:00Z","timestamp":1611619200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T00:00:00Z","timestamp":1611619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003655","name":"National Institute of Food and Drug Safety Evaluation","doi-asserted-by":"publisher","award":["16183MFDS541"],"award-info":[{"award-number":["16183MFDS541"]}],"id":[{"id":"10.13039\/501100003655","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Big Data"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Some of the variants detected by high-throughput sequencing (HTS) are often not reproducible. To minimize the technical-induced artifacts, secondary experimental validation is required but this step is unnecessarily slow and expensive. Thus, developing a rapid and easy to use visualization tool is necessary to systematically review the statuses of sequence read alignments. Here, we developed a high-performance alignment capturing tool, CaReAl, for visualizing the read-alignment status of nucleotide sequences and associated genome features. CaReAl is optimized for the systematic exploration of regions of interest by visualizing full-depth read-alignment statuses in a set of PNG files. CaReAl was 7.5 times faster than IGV \u2018snapshot\u2019, the only stand-alone tool which provides an automated snapshot of sequence reads. This rapid user-programmable capturing tool is useful for obtaining read-level data for evaluating variant calls and detecting technical biases. The multithreading and sequential wide-genome-range-capturing functionalities of CaReAl aid the efficient manual review and evaluation of genome sequence alignments and variant calls. CaReAl is a rapid and convenient tool for capturing aligned reads in BAM. CaReAl facilitates the acquisition of highly curated data for obtaining reliable analytic results.<\/jats:p>","DOI":"10.1186\/s40537-021-00418-w","type":"journal-article","created":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T05:03:36Z","timestamp":1611637416000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["CaReAl: capturing read alignments in a BAM file rapidly and conveniently"],"prefix":"10.1186","volume":"8","author":[{"given":"Yoomi","family":"Park","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heewon","family":"Seo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyunghun","family":"Yoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ju Han","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,1,26]]},"reference":[{"issue":"4","key":"418_CR1","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1016\/j.molcel.2015.05.004","volume":"58","author":"JA Reuter","year":"2015","unstructured":"Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58(4):586\u201397.","journal-title":"Mol Cell"},{"issue":"12","key":"418_CR2","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1161\/CIRCRESAHA.113.300939","volume":"112","author":"JM Churko","year":"2013","unstructured":"Churko JM, Mantalas GL, Snyder MP, Wu JC. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res. 2013;112(12):1613\u201323.","journal-title":"Circ Res"},{"issue":"1","key":"418_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ygeno.2015.11.003","volume":"107","author":"JM Heather","year":"2016","unstructured":"Heather JM, Chain B. The sequence of sequencers: the history of sequencing DNA. 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