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InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
Lai, Binbin1,2,3; Wang, Fumeng1,2; Wang, Xiaoqi1,2; Duan, Liping4; Zhu, Huaiqiu1,2
刊名BMC BIOINFORMATICS
2015-08-07
DOI10.1186/s12859-015-0686-x
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
WOS记录号WOS:000359100000001
项目编号2012BAI06B02 ; 30970667 ; 11021463 ; 61131003 ; 91231119 ; 2011CB707500 ; YB 20101000102
资助机构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
引用统计
被引频次:4[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/54277
专题北京大学第三临床医学院_消化科
北京大学医学部管理机构_科学研究处
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
推荐引用方式
GB/T 7714
Lai, Binbin,Wang, Fumeng,Wang, Xiaoqi,et al. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads[J]. BMC BIOINFORMATICS,2015,16.
APA Lai, Binbin,Wang, Fumeng,Wang, Xiaoqi,Duan, Liping,&Zhu, Huaiqiu.(2015).InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.BMC BIOINFORMATICS,16.
MLA Lai, Binbin,et al."InteMAP: Integrated metagenomic assembly pipeline for NGS short reads".BMC BIOINFORMATICS 16(2015).
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