population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data
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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/28 10:33] – created bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 14:53] – [Qiime2 data filtering and feature (OTU) table construction] bngina | ||
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+ | ====== Analysis of Microbiome data ====== | ||
+ | Micriobial analysis aims to understand microbes and their functions in their environments. [[https:// | ||
- | QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers | + | We outline a pipeline to analyse 16S/18S paired-end sequencing data. Qiime2 can be used to analyse single-end and paired-end data. |
+ | |||
+ | ==== Importing data into Qiime2 ==== | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ | We import raw fastq files into qiime2. Depending on the sequencing platform used to generate the data, you will have data that has been de-multiplexed into sample specif fastq files, or not. The MiSeq platform at [[ https:// | ||
+ | |||
+ | Read more about [[ https:// | ||
+ | |||
+ | To import fastq files; | ||
+ | |||
+ | < | ||
+ | |||
+ | #i create | ||
+ | |||
+ | mkdir / | ||
+ | |||
+ | #import the fastq files | ||
+ | |||
+ | qiime tools import \ | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, | ||
+ | |||
+ | < | ||
+ | |||
+ | qiime demux summarize \ | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | ==== Qiime2 data filtering and feature (OTU) table construction ==== | ||
+ | |||
+ | Qiime2 provides two pluggins/ | ||
+ | |||
+ | Important | ||
+ | |||
+ | === Dada2 === | ||
+ | |||
+ | The Dada2 pipeline detects and corrects illumina amplicon | ||
+ | To see usage and parameters that can be adjusted get the help for the pluggin i.e | ||
+ | |||
+ | < | ||
+ | qiime dada2 --help | ||
+ | </ | ||
+ | |||
+ | The data we are using is paired-end, hence we will use the [[https:// | ||
+ | |||
+ | A key parameter to be careful about is the //'' | ||
+ | |||
+ | The other key parameters in quality | ||
+ | |||
+ | To determine what values to pass for these two parameters; | ||
+ | *Review the Interactive Quality Plot tab in the //'' | ||
+ | *The expected fragment size after the reads are joined, particularly for the //'' |
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina