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De novo construction of a Gene-space for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources

机译：通过使用有限的计算资源进行NGS读段的提取和组装的迭代过程（iPEA协议）从头构建富含重复序列的二倍体植物基因组的基因空间

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BackgroundThe continuing increase in size and quality of the “short reads” raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a significant challenge due to the large number of repeated sequences which are problematic for a whole-genome quality de novo assembly. Furthermore, for most SNP identification approaches in plant genetics and breeding, only the “Gene-space” regions including the promoter, exon and intron sequences are considered.

机译：背景技术“短读”原始数据的大小和质量的持续增加，对于通过各种生物信息学工具获得的装配质量具有重要的帮助。然而，由于大量重复序列对于全基因组从头组装是有问题的，因此为大多数植物建立参考基因组序列仍然是一项重大挑战。此外，对于植物遗传学和育种中的大多数SNP鉴定方法，仅考虑“基因空间”区域，包括启动子，外显子和内含子序列。

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期刊名称 BMC Research Notes
作者
Christelle Aluome; Grégoire Aubert; Susete Alves Carvalho; Marie-Christine Le Paslier; Judith Burstin; Dominique Brunel;
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作者单位

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年(卷),期 2016(9),-1
年度 2016
页码 81
总页数 9
原文格式 PDF
正文语种
中图分类
关键词
Gene-space Unigene Next-generation sequencing NGS Assembly Iterative process Limited computing resources;

机译：基因空间;Unigene;下一代测序NGS;组装;迭代过程;有限的计算资源;

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专利

1. Combination of de novo assembly of massive sequencing reads with classical repeat prediction improves identification of repetitive sequences in Schistosoma mansoni. [J] . Lepesant JM, Roquis D, Emans R, Experimental parasitology . 2012,第4期

机译：大规模测序读数的从头组装与经典重复预测相结合，可改善曼氏血吸虫中重复序列的鉴定。
2. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences [J] . Shairul Izan, Danny Esselink, Richard G. F. Visser, Frontiers in Plant Science . 2017,第12期

机译：<斜视> de novo 从非模型物种的完全叶绿体基因组组装从基于k-mer频率的叶绿体中的叶绿体中的总DNA序列读取
3. Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads [J] . Faber-Hammond Joshua J., Brown Kim H. Human Genetics . 2016,第7期

机译：人类基因组的锚定伪-从头装配可从未映射的序列读取中识别出广泛的序列变异
4. Scaling short read de novo DNA sequence assembly to gigabase genomes. [D] . Cook, Jeffrey J. 2011

机译：将短读从头DNA序列组装扩展到gigabase基因组。
5. Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly [O] . Tsunglin Liu, Cheng-Hung Tsai, Wen-Bin Lee, -1

机译：优化下一代测序（NGS）阅读中的信息以改善De Novo基因组装配
6. De novo construction of a “Gene-space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources [O] . 2016

机译：通过使用有限的计算资源进行NGS读段的提取和组装的迭代过程（iPEA协议）从头构建富含重复序列的二倍体植物基因组的“基因空间”

De novo construction of a Gene-space for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources

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