Russian Journal of Biological Physics and Chemisrty Russian Journal of Biological Physics and Chemisrty АКТУАЛЬНЫЕ ВОПРОСЫ БИОЛОГИЧЕСКОЙ ФИЗИКИ И ХИМИИ 2499-9962 54569 Общая биофизика General biophysics Общая биофизика Influence of the degree of sequencing data filtering on the quality and completeness of the de novo transcriptome assembly Влияние степени фильтрации данных секвенирования на качество и полноту de novo сборки транскриптома Мегер Я В Meger Y V meger_yakov@mail.ru Лантушенко А О Lantushenko A O Водясова Е А Vodiasova E A Севастопольский государственный университет ru Sevastopol State University ru Севастопольский государственный университет ru Sevastopol State University ru Севастопольский государственный университет; ФИЦ «Институт биологии южных морей им. А.О. Ковалевского» ru Sevastopol State University; A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS ru 25 12 2020 25 12 2020 5 4 580 586 20 12 2020 20 12 2020 https://rusjbpc.ru/en/nauka/article/54569/view

Для сборки de novo транскриптома существует множество сборщиков, которые имеют различающиеся алгоритмы. В тоже время этап фильтрации, являясь одним из ключевых, также имеет несколько подходов и алгоритмов. Однако, на сегодняшний день работ по изучению влияния степени фильтрации на сборку de novo транскриптома крайне мало. В данной работе были проанализированы транскриптомы, полученные с помощью двух наиболее распространенных программ (rnaSPADES и Trinity), а также применены различные подходы к этапу фильтрации прочтений. Были показаны ключевые различия для двух сборок и выявлены параметры, которые оказались чувствительными к степени фильтрации и длине входных прочтений. Также был предложен эффективный алгоритм фильтрации, который является двухэтапным и позволяет максимально сохранить объем входных данных при необходимом качестве всех прочтений после фильтрации и обрезки.

There are many assemblers that have different algorithms to assemble a de novo transcriptome. At the same time, the filtering stage, being one of the key stages, also has several approaches and algorithms. However, to date, there is very little work on the influence of filtration degree on the de novo transcriptome Assembly. In this paper, we analyzed transcripts obtained using two of the most common programs (rnaSPADES and Trinity), and applied various approaches to the stage of filtering readings. Key differences were shown for the two assemblies and parameters were identified that were sensitive to the degree of filtering and the length of input reads. We also proposed an effective filtering algorithm that is two-stage and allows you to save the maximum amount of input data with the necessary quality of all readings after filtering and cropping.

 rnaSPADES Trinity сборка de novo транскриптома RNA-seq фильтрация прочтений RNA-seq rnaSPADES Trinity de novo transcriptome assembly read filtering Работа выполнена в рамках государственной бюджетной темы (№ 0828-2018-0003), при поддержке Министерства образования и науки РФ (грант № 14.W03.31.0015) и внутреннего гранта СевГУ 2020 № 33/06-31.

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