QIIME2 use

Activation qiime2 execution environment: source activate qiime2-2019.4 
how to view conda existing environment: conda info -e 

following analysis Process Reference: https: //docs.qiime2.org/2019.4/tutorials/qiime2-for-experienced-microbiome- researchers /

1, data preparation

Now we often is the data in this format, each sample pair of data files

wget \
  -O "casava-18-paired-end-demultiplexed.zip" \
  "https://data.qiime2.org/2019.4/tutorials/importing/casava-18-paired-end-demultiplexed.zip" 

download, unzip the file in the folder as follows:

 

2, converts the data format to qza (qiime their newly defined type of format, meaning little programming object)

Import price Tools \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path casava-18-paired-end-demultiplexed \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \ Paired-path-DEMUX --output-end.qza

 . 3, view data quality
qiime demux summarize --i-data demux-
see the results with the following command:
qiime tools view demux-summary-1.qzv

4, combined into a single two-terminal end of the sequence

qiime dada2 denoise-paired --p-trim-left-f 9 --p-trim-left-r 9 --p-trunc-len-f 10 --p-trunc-len-r 10 --i-demultiplexed-seqs demux-paired-end.qza --o-representative-sequences demux-paired-end-denoise.qza --o-table table-1.qza --o-denoising-stats stats-1.qza

 

4, the data is cut

qiime dada2 denoise-paired --p-trim-left-f 9 --p-trim-left-r 9 --p-trunc-len-f 10 --p-trunc-len-r 10 --i-demultiplexed-seqs demux-paired-end.qza --o-representative-sequences demux-paired-end-denoise.qza --o-table table-1.qza --o-denoising-stats stats-1.qza

 

https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313