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An automated method for bacterial community composition and diversity analysis of 16S rRNA genes

A diversity analysis and community technology, applied in the fields of molecular biology and high-throughput sequencing data analysis, can solve the problems of inability to meet the analysis needs of researchers, different sequencing depths, and data leveling processing, so as to reduce the workload and analyze The results are comprehensive and the effect of eliminating analysis errors

Active Publication Date: 2019-02-12
SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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Problems solved by technology

In some cases, the analytical needs of researchers cannot be met
In addition, the original analysis process does not flatten the data when performing subsequent comparative analysis such as PCA and PCoA, which will introduce analysis errors caused by different sequencing depths

Method used

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  • An automated method for bacterial community composition and diversity analysis of 16S rRNA genes

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Embodiment Construction

[0052] In a specific embodiment, the method is as figure 1 The following steps are shown:

[0053] Step 1: For the original paired-end sequencing data of the Illumina Miseq platform, execute the MiSeqQuality16S.pl script with the original off-machine data as input data, the window size is 10bp, and the step size is 1bp, starting from the first base position at the 5' end, The average quality of the bases in the window is required to be ≥ Q20 (that is, the average sequencing accuracy of the bases is ≥ 99%), and the sequence is truncated from the first window whose average quality value is lower than Q20, and the length of the truncated sequence is required to be ≥ 150bp, and no Ambiguity base N is allowed. Then, use the FLASH software to pair and join the double-ended sequences that have passed the quality screening according to the overlapping bases: the overlapping base length of the two sequences of Read 1 and Read 2 is required to be ≥ 10 bp, and base mismatching is not al...

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Abstract

The present invention discloses an automated method for bacterial community composition and diversity analysis of 16S rRNA genes. The 16S rRNA sequencing data analysis process provided by it uses sequencing raw sequence data as input, and calls industry-standard analysis tools (such as: Mothur , QIIME, etc.), and finally visualize the data and get easy-to-interpret analysis results. The present invention includes the current popular mainstream analysis items, and at the same time, the analysis content is modularized, the methods of data mining and analysis are more diverse and deeper, and different analysis module contents can be combined according to different needs, and the sequential flow arrangement is also more reasonable ; In addition, analysis errors caused by different sequencing depths are eliminated, making the analysis results more comprehensive, accurate and reliable.

Description

Technical field: [0001] The present invention generally relates to the technical field of molecular biology, in particular to the technical field of high-throughput sequencing data analysis, and more specifically, relates to an automated method for bacterial community composition and diversity analysis of 16S rRNA genes. Background technique: [0002] The new generation of high-throughput sequencing technology has greatly reduced the time and cost of sequencing, making large-scale sequencing gradually become a routine research and detection method, and the amount of data generated by sequencing has increased dramatically. How to efficiently analyze these data has become an urgent problem to be solved. [0003] At present, there are many high-throughput sequencing data analysis tools, and the bioinformatics tools for analyzing sequence information are complex. For large-scale sequencing data analyzing the microecology of flora, a variety of mature analysis tools have also bee...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 薛正晟寇文伯王慧娟姜丽荣孙子奎
Owner SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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