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学科主题: 临床医学
题名:
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
作者: Lai, Binbin1,2,3; Wang, Fumeng1,2; Wang, Xiaoqi1,2; Duan, Liping4; Zhu, Huaiqiu1,2
刊名: BMC BIOINFORMATICS
发表日期: 2015-08-07
DOI: 10.1186/s12859-015-0686-x
卷: 16
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology
类目[WOS]: Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
研究领域[WOS]: Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
关键词[WOS]: DE-NOVO ASSEMBLER ; SINGLE-CELL ; LARGE GENOMES ; ALGORITHMS ; PREDICTION ; CATALOG ; VELVET
英文摘要:

Background: Next-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads generated by sequencers such as Illumina. To date, how to generate a high-quality draft assembly for metagenomic sequencing projects has not been fully addressed.

Results: We conducted a comprehensive assessment on state-of-the-art de novo assemblers and revealed that the performance of each assembler depends critically on the sequencing depth. To address this problem, we developed a pipeline named InteMAP to integrate three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision of which assembling approaches to use according to the sequencing coverage estimation algorithm for each short read, the pipeline presents an automatic platform suitable to assemble real metagenomic NGS data with uneven coverage distribution of sequencing depth. By comparing the performance of InteMAP with current assemblers on both synthetic and real NGS metagenomic data, we demonstrated that InteMAP achieves better performance with a longer total contig length and higher contiguity, and contains more genes than others.

Conclusions: We developed a de novo pipeline, named InteMAP, that integrates existing tools for metagenomics assembly. The pipeline outperforms previous assembly methods on metagenomic assembly by providing a longer total contig length, a higher contiguity and covering more genes. InteMAP, therefore, could potentially be a useful tool for the research community of metagenomics.

语种: 英语
所属项目编号: 2012BAI06B02 ; 30970667 ; 11021463 ; 61131003 ; 91231119 ; 2011CB707500 ; YB 20101000102
项目资助者: National Key Technology Research and Design Program of China ; National Natural Science Foundation of China ; National Basic Research Program of China ; Excellent Doctoral Dissertation Supervisor Funding of Beijing
WOS记录号: WOS:000359100000001
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.bjmu.edu.cn/handle/400002259/54277
Appears in Collections:北京大学第三临床医学院_消化科_期刊论文

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作者单位: 1.Peking Univ, Coll Engn, State Key Lab Turbulence & Complex Syst, Beijing 100871, Peoples R China
2.Peking Univ, Coll Engn, Dept Biomed Engn, Beijing 100871, Peoples R China
3.Peking Univ, Ctr Quantitat Biol, Beijing 100871, Peoples R China
4.Peking Univ, Hosp 3, Dept Gastroenterol, Beijing 100191, Peoples R China

Recommended Citation:
Lai, Binbin,Wang, Fumeng,Wang, Xiaoqi,et al. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads[J]. BMC BIOINFORMATICS,2015,16.
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