Вычислительные проблемы анализа ошибок коротких прочтений ДНК при секвенировании следующего поколения

Секвенирование следующего поколения (NGS) с помощью коротких прочтений ДНК вносит большой вклад в решение задач современной геномики, генетики, клеточной биологии и медицины, особенно в исследования метагеномики, сравнительной геномики, определение полиморфизмов, скрининг мутаций, транскриптомное профилирование, изучение ремоделирования хроматина и многие другие приложения. Секвенирование неустойчиво к техническим ошибкам, которые могут влиять на научные выводы. NGS технологии состоят из создания коллекции многочисленных коротких фрагментов ДНК, именуемой «библиотекой», получения молекулярных колоний и их дальнейшего массового параллельного секвенирования. Такие секвенированные фрагменты называются «прочтениями», они собираются (ассемблируются) в протяженные строки. Протяженные последовательности, в свою очередь, собираются в геномы для дальнейшего анализа. Вычислительные/процессинговые ошибки и сбои секвенирования – это ошибки, возникающие при последующей цифровой обработке секвенированных образцов. Последующая обработка (процессирование) включает процедуры оценки качества, картирования, ассемблирования и даже корректировки ошибочных данных. Данная статья рассматривает вычислительные ошибки процессирования, компьютерные и статистические подходы для их определения, а также представляет словарь терминологии секвенирования. Рассмотрены задачи идентификации мутаций («Определение вариаций») в данных секвенирования и контроль качества их определения. Определение вариаций включает локальные вариации, такие как одиночные нуклеотидные полиморфизмы, короткие вставки и делеции (инделы), и масштабные вариации (инверсии, транслокации или большие инделы). Обсуждены проблемы контроля качества исходных (сырых) данных, ошибки, возникающие на этапах выравнивания прочтений последовательностей ДНК на референсный геном и последующего выравнивания/ассемблирования.

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