Targeted Gene Metagenomic Data Analysis    ◾    279

--p-allowmergestagger \

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

For checking the merging, run “demux summarize” to create a visualization file for the

summary and quality of the merged reads as discussed above.

qiime demux summarize \

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

--o-visualization viz/demux-yoga-merged-qc.qzv

qiime tools view viz/demux-yoga-merged-qc.qzv

If you open Interactive quality plot on the summary report, you will notice that the for-

ward and reverse reads have been joined as shown in Figure 7.9.

If, at this point, you notice that the forward reads (for single-end data) or merged reads

(for paired-end data) require filtering, you can then perform that with “quality-filter

q-score” as follows:

qiime quality-filter q-score \

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

--o-filtered-sequences inputs/demux-yoga-merged-filter.qza \

--o-filter-stats inputs/demux-yoga-merged-filter-stats.qza

7.3.4.2.1.2  Sequence Dereplication

Before clustering, the reads must be dereplicated to reduce the redundancy of the reads

based on similarity. The dereplication is carried out with “dereplicate-sequences” method

FIGURE 7.9  Per base quality plots of the merged yoga data.