Differences

This shows you the differences between two versions of the page.

--- 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 [2020/03/30 14:49] – bngina
@@ Line 1: / Line 1: @@
+====== Analysis of Microbiome data ======
+Micriobial analysis aims to understand microbes and their functions in their environments. [[https://docs.qiime2.org/2020.2/tutorials/overview/| QIIME2]] (**Q**uantitative **I**nsights **I**nto **M**icrobial **E**cology) is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.
+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://docs.qiime2.org/2020.2/concepts/|Data]] used and produced by qiime2 are stored as artifacts. Artifacts contain data and metadata and have a ''.qza'' extension. Qiime2 provides methods to view information (data and metadata) stored in artifacts by creating visualizations, that have a ''.qzv'' extension.
+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://hub.africabiosciences.org/| BecA-ILRI Hub]] will de-multiplex the data and we get sample specific fastq files.
+Read more about [[ https://docs.qiime2.org/2020.2/tutorials/importing/|different data types and importing them into qiime2]] for anlaysis. We will be importing data described as type //Cassava 1.8 paired-end de-multiplexed fastq//.
+To import fastq files;
+<code>
+#i create a directory to store all my artifact i.e '.qza' and the related visualization i.e '.qzv' files.
+mkdir /home/mydir/qiime2_data/
+#import the fastq files
+qiime tools import \
+ --type 'SampleData[PairedEndSequencesWithQuality]' \
+ --input-path /home/mydir/qiime2_data/ \
+ --input-format CasavaOneEightSingleLanePerSampleDirFmt \
+ --output-path /home/mydir/qiime2_data/my_raw_data.qza
+</code>
+We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, .qzv, files. The ''.qzv''  files can be opened on any browser using [[https://view.qiime2.org/ |qiime viewer]]. To create visualization for the imported data;
+<code>
+qiime demux summarize \
+ --i-data  /home/mydir/qiime2_data/my_raw_data.qza \
+ --o-visualization /home/mydir/qiime2_data/my_raw_data.qzv
+</code>
+==== Qiime2 data filtering and feature (OTU) table construction ====
+Qiime2 provides two pluggins/methods for filtering your sequences to the required quality and length and from these construct featuretables better known as OTU tables and the representative feature sequences. These are [[https://www.ncbi.nlm.nih.gov/pubmed/27214047| Dada2]] and [[ https://msystems.asm.org/content/2/2/e00191-16| Deblur]].
-QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results