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MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing

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Abstract

Reads classification is an important fundamental problem in metagenomics study. With the development of next-generation sequencing, metagenome samples can be generated using much less money and time. However, the short reads generated by next-generation sequencing make the problem of reads classification much more difficult than before. None of the existing tools can assign NGS short reads to each genome accurately, which limit their use in real application. Fortunately, in many applications, it is meaningless to separate all the species in the metagenome sample from each other. That is because we usually only focus on some specified species categories in the sample and do not care about the others. There is no existing tool that is designed technically for obtaining specified species from short metagenome reads generated by next-generation sequencing. In this paper, we propose a tool named MetaObtainer to obtain the specified species from next-generation sequencing short reads. The tool synthesizes some of newest technologies for processing of short reads, so it can have better performance than other tools. It can (1) deal with next-generation sequencing reads which are shorter than 100 bp with very high accuracy (both of precision and recall are more than 90 %); (2) find unknown species using the reference genomes of species which are similar with it; (3) perform well when reads of specified species are very few in the dataset; (4) handle genomes of similar abundance levels as well as different abundance levels (1:10); and (5) obtain multiple species categories from metagenome sample.

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Acknowledgments

We thank Jiaoyun Yang, Pengyu Nie, and Xingxing Zhang, who provided many helpful suggestions for our article. Constructive comments from the reviewers are also appreciated. This work is supported by the National Natural Science Foundation of China (No. 61033009 and No. 60970085) and Foreign Scholars in University Research and Teaching Programs (B07033).

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Authors and Affiliations

  1. School of Computer Science and Technology, University of Science and Technology of China, Hefei, 230027, China

    Weihua Pan, Bo Chen & Yun Xu

  2. Anhui Province-MOST Co-Key Laboratory of High Performance Computing and Its Application, University of Science and Technology of China, Hefei, 230027, China

    Weihua Pan, Bo Chen & Yun Xu

Authors
  1. Weihua Pan
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  2. Bo Chen
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  3. Yun Xu
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Correspondence to Yun Xu.

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Pan, W., Chen, B. & Xu, Y. MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing. Interdiscip Sci Comput Life Sci 7, 405–413 (2015). https://doi.org/10.1007/s12539-015-0281-x

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  • DOI: https://doi.org/10.1007/s12539-015-0281-x

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