{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T03:26:44Z","timestamp":1772249204537,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2020,7,13]],"date-time":"2020-07-13T00:00:00Z","timestamp":1594598400000},"content-version":"vor","delay-in-days":12,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004285","name":"St. Petersburg State University","doi-asserted-by":"publisher","award":["51555639"],"award-info":[{"award-number":["51555639"]}],"id":[{"id":"10.13039\/501100004285","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/ablab\/TandemTools.<\/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\/btaa440","type":"journal-article","created":{"date-parts":[[2020,5,4]],"date-time":"2020-05-04T08:13:01Z","timestamp":1588579981000},"page":"i75-i83","source":"Crossref","is-referenced-by-count":54,"title":["TandemTools: mapping long reads and assessing\/improving assembly quality in extra-long tandem repeats"],"prefix":"10.1093","volume":"36","author":[{"given":"Alla","family":"Mikheenko","sequence":"first","affiliation":[{"name":"Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University , Saint Petersburg 199034, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrey V","family":"Bzikadze","sequence":"additional","affiliation":[{"name":"Graduate Program in Bioinformatics and Systems Biology, University of California , San Diego, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexey","family":"Gurevich","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University , Saint Petersburg 199034, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen H","family":"Miga","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavel A","family":"Pevzner","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California , San Diego, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,7,13]]},"reference":[{"key":"2024021913372535300_btaa440-B1","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btv688","article-title":"hybridSPAdes: an algorithm for hybrid assembly of short and long reads","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"2024021913372535300_btaa440-B2","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1101\/gr.078303.108","article-title":"Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties","volume":"18","author":"Bacolla","year":"2008","journal-title":"Genome Res"},{"key":"2024021913372535300_btaa440-B3","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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