284    ◾    Bioinformatics

qiime metadata tabulate \

--m-input-file dada2/stats_yoga_dada2.qza \

--o-visualization dada2/stats_yoga_dada2.qzv

qiime tools view dada2/stats_yoga_dada2.qzv

The DADA2 stats summary table is a TSV. It shows the ID, number of input reads, number

of reads filtered, percentage of reads passed the filter, number of denoised reads, number of

merged reads, percentage of reads merged, number of non-chimeric reads, and percentage

of non-chimeric reads for each sample in the study.

7.3.4.2.2.2  Denoising with Deblur

Deblur plugin denoises single-end reads and merged paired-end read. Paired-end sequences

must be merged using “vsearch join-pairs”, as shown above, before being denoised by

deblur.

mkdir deblur

qiime vsearch join-pairs \

--i-demultiplexed-seqs inputs/demux-yoga.qza \

--p-allowmergestagger \

--o-joined-sequences deblur/demux-yoga-merged.qza

It is recommended to run quality assessment and quality control by filtering low-quality

reads using “quality-filter q-score” before denoising with deblur.

qiime quality-filter q-score \

--i-demux inputs/demux-yoga-merged.qza \

--o-filtered-sequences deblur/demux-yoga-merged-filtered.qza \

--o-filter-stats deblur/demux-yoga-merged-filtered-stat.qza

Denoising with deblur is carried out with “q2-deblur” plugin, which has two methods:

“denoise-16S” for denoising 16S rRNA gene sequences and “denoise-other” for denoising

other types of targeted gene sequences. When you use “denoise-16S”, deblur will perform

an initial positive filtering step by discarding any reads that do not have a minimum 60%

identity similarity to database sequences from the 85% GreenGenes.

You can use “deblur denoise-16S” method, which has “--p-trim-length” parameter that

can be set to truncate the reads at specific position for quality filtering or you can set that

parameter to -1 to disable trimming. The following script will perform deblur denoising:

mkdir deblur

qiime deblur denoise-16S \

--i-demultiplexed-seqs deblur/demux-yoga-merged.qza \

--p-trim-length -1 \

--p-jobs-to-start 4 \

--p-sample-stats \

--o-representative-sequences deblur/rep-seqs_yoga_deblur.qza \