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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/VJ21.004</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-2913</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>БИОИНФОРМАТИКА И СИСТЕМНАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>BIOINFORMATICS AND COMPUTATIONAL SYSTEMS BIOLOGY</subject></subj-group></article-categories><title-group><article-title>Улучшение качества сборки de novo транскриптомов ячменя на основе гибридного подхода для линий с изменениями окраски колоса и стебля</article-title><trans-title-group xml:lang="en"><trans-title>Improving the quality of barley transcriptome de novo assembling by using a hybrid approach for lines with varying spike and stem coloration</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Шмаков</surname><given-names>Н. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Shmakov</surname><given-names>N. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><email xlink:type="simple">shmakov@bionet.nsc.ru</email><xref ref-type="aff" rid="aff-1"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр, Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomics Center, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2021</year></pub-date><pub-date pub-type="epub"><day>15</day><month>03</month><year>2021</year></pub-date><volume>25</volume><issue>1</issue><fpage>30</fpage><lpage>38</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Шмаков Н.А., 2021</copyright-statement><copyright-year>2021</copyright-year><copyright-holder xml:lang="ru">Шмаков Н.А.</copyright-holder><copyright-holder xml:lang="en">Shmakov N.A.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/2913">https://vavilov.elpub.ru/jour/article/view/2913</self-uri><abstract><p>Реконструкция транскриптома de novo – важная стадия биоинформатического анализа данных RNA-seq, которая позволяет получить последовательности транскриптов, присутствующих в изучаемом биологическом образце. Наличие точной и полной последовательности транскриптома организма, в свою очередь, является необходимым условием для дальнейшей работы с данными RNA-seq. Биоинформатическим сообществом было создано множество программ-сборщиков для реконструкции транскриптома из коротких прочтений RNA-seq. Сборщики позволяют проводить как de novo реконструкцию транскриптома, так и реконструкцию, основанную на картировании коротких прочтений RNA-seq на последовательность референсного генома организма. Большинство de novo сборщиков, работающих с данными RNA-seq, применяют технологию реконструкции последовательностей методом графов де Брёйна. Однако детали их работы могут существенно различаться, поэтому различия могут встречаться и в результатах. Некоторые авторы рекомендуют для получения более полной и качественной сборки использовать гибридную сборку транскриптома – подход, основанный на комбинации результатов работы нескольких сборщиков. Преимущество такого подхода было продемонстрировано в ряде исследований по анализу транскриптомов на платформе Illumina. Нами предложен гибридный подход по созданию сборок транскриптома ячменя Hordeum vulgare изогенной линии Bowman и двух почти изогенных линий, полученных на основе Bowman и контрастных по окраске колоса, используя данные, полученные при секвенировании матричной РНК на платформе IonTorrent. В данном подходе применяются несколько индивидуальных сборщиков: Trans-ABySS, rnaSPAdes и Trinity. Были оценены некоторые показатели, характеризующие полноту и точность сборки: доля обнаруженных в сборке известных транскриптов ячменя, доля задействованных в сборке прочтений из библиотек RNA-seq, значение критерия BUSCO. По совокупности этих показателей метасборки демонстрируют более высокое качество полученного транскриптома по сравнению с индивидуальными сборщиками.</p></abstract><trans-abstract xml:lang="en"/><kwd-group xml:lang="ru"><kwd>RNA-seq</kwd><kwd>транскриптомика</kwd><kwd>de novo реконструкция транскриптома</kwd><kwd>IonTorrent</kwd></kwd-group><kwd-group xml:lang="en"><kwd>RNA-seq</kwd><kwd>transcriptomics</kwd><kwd>de novo transcriptome reconstruction</kwd><kwd>IonTorrent</kwd></kwd-group><funding-group xml:lang="en"><funding-statement>The work was supported by Russian Science Foundation project No. 18-14-00293 (problem statement, algorithm creation, data analysis). 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