Тип публикации: доклад, тезисы доклада, статья из сборника материалов конференций
Конференция: International Multiconference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BDRS\SB); Novosibirsk, RUSSIA; Novosibirsk, RUSSIA
Год издания: 2019
Идентификатор DOI: 10.1186/s12859-018-2570-y
Ключевые слова: de novo genome assembly, Siberian larch, Larix sibirica, Forestry, Numerical methods, Arabidopsis thaliana, De novo assemblies, Genome assembly, Nucleotide sequences, Pinus lambertiana, Pseudotsuga menziesii, Genes, article, Douglas fir, genome, human, Larix
Аннотация: BackgroundDe novo assembling of large genomes, such as in conifers (similar to 12-30 Gbp), which also consist of similar to 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA asПоказать полностьюsemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.ResultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.ConclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii. Background: De novo assembling of large genomes, such as in conifers (~ 12-30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computin
Журнал: BMC BIOINFORMATICS
Выпуск журнала: Vol. 20
Номера страниц: 37
ISSN журнала: 14712105
Место издания: LONDON
Издатель: BMC