Quality filtering

Quality overview

We can get an overview of the read quality by using the summarize action from the demux QIIME 2 plugin. This command will generate a visualization of the quality scores at each position. You can learn more about this action in the QIIME 2 documentation.

mosh demux summarize \
    --i-data ./cache:reads \
    --o-visualization demux.qzv

To see an example of the visualization you can go here.

Read trimming and quality filtering

In order to remove low quality bases from the reads, we can use one of the trim actions from the cutadapt QIIME 2 plugin. Here we are using the trim-paired action to remove all the reads shorter than 90 bp:

mosh cutadapt trim-paired \
    --i-demultiplexed-sequences ./cache:reads \
    --p-minimum-length 90 \
    --o-trimmed-sequences ./cache:reads_trimmed