This community tutorial has been migrated to our official documentation. Please refer to that tutorial instead.
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This tutorial covers paired end read analysis in QIIME 2. It was developed and tested with the QIIME 2 2017.11 release. QIIME 2 releases prior to 2017.11 are not compatible with this tutorial.
Note: This tutorial does not cover read-joining and denoising with DADA2. Instead, this tutorial focuses on alternative approaches to analyzing paired end reads in QIIME 2. If you are interested in joining and denoising reads with DADA2, the Atacama soil microbiome tutorial illustrates how to use qiime dada2 denoise-paired for this purpose. If you plan to use DADA2 to join and denoising your paired end data, do not join your reads prior to denoising with DADA2; DADA2 expects reads that have not yet been joined, and will join the reads for you during the denoising process.
In QIIME 2, we use the term single end reads to refer to forward or reverse reads in isolation; we use the term paired end reads to refer to forward and reverse reads that have not yet been joined; and we use the term joined reads to refer to forward and reverse reads that have already been joined (or merged). It is important to understand which of these terms apply to your data, as this will determine what steps are necessary to analyze your paired end data.
It is currently possible to join paired end reads in QIIME 2 using the q2-vsearch plugin, or to import reads that have been joined outside of QIIME 2 (for example, with fastq-join). This tutorial will cover both of these processes.
Joining reads and analyzing joined reads
First, we'll join paired end reads with QIIME 2. Begin by downloading the following SampleData[PairedEndSequencesWithQuality] artifact, which contains the demultiplexed reads from the Atacama soil microbiome tutorial.
Joining reads
Next, use the join-pairs method in the q2-vsearch plugin to join the reads:
qiime vsearch join-pairs \
--i-demultiplexed-seqs demux.qza \
--o-joined-sequences demux-joined.qza
Viewing summary of joined data with read quality
You can next generate a summary of the demux-joined.qza artifact.
qiime demux summarize \
--i-data demux-joined.qza \
--o-visualization demux-joined.qzv
This summary is particularly useful for determining approximately how long your joined reads are (we'll come back to this when we denoise with Deblur). When looking at the quality plots in this visualization, if you hover over a specific position you'll see how many reads are at least that long (of the reads that were sampled for computing sequence quality). Make note of the highest sequence position where most (say, > 99%) of your reads are at least that long.
For example, when hovering over a black box in this visualization (which is generated from a larger data set than the one used in this tutorial), I see that 10000 out of the 40126 sequences were used to estimate the quality score distribution at this position.
When I hover over position 250, which is illustrated with a red box, I see that some sequences are not this long because only 9994 sequences were used for estimating the quality score distribution at this position. The red box and the red text below tell me that some sequences were not at least this long.
When I hover over position 254, which is also illustrated with a red box, I see that many sequences are not this long because only 845 sequences were used for estimating the quality score distribution at this position.
Based on a comparison of these plots, I will note that most of my sequences are at least 250 bases long. We plan to simplify this process in the near future (see add seven-number summary of read length distribution to `summarize` · Issue #71 · qiime2/q2-demux · GitHub).
Sequence quality control
Next we'll apply quality control to our sequences using quality-filter q-score-joined. This method is identical to quality-filter q-score, except that it operated on joined reads. The parameters to this method have not been extensively benchmarked on joined read data, so we recommend experimenting with different parameter settings.
qiime quality-filter q-score-joined \
--i-demux demux-joined.qza \
--o-filtered-sequences demux-joined-filtered.qza \
--o-filter-stats demux-joined-filter-stats.qza
At this stage you can choose to proceed using Deblur for additional quality control, or you can dereplicate sequences and optionally cluster them into OTUs with q2-vsearch. Deblur should give much higher quality results, so we recommend that procedure and will illustrate that approach in the next steps of this tutorial.
If you are instead interested in experimenting with an analysis workflow that is more like QIIME 1 processing (for example, to compare your Deblur or DADA2 result with a QIIME 1-like pipeline), you should next dereplicate and cluster your sequences. If you try this option, we strongly encourage you to call qiime quality-filter q-score-joined with a higher min-quality threshold - possibly --p-min-quality 20 or --p-min-quality 30. You can then follow the steps in the OTU clustering tutorial. After clustering, you will likely want to filter features that are observed in only one sample using qiime feature-table filter-features --p-min-samples.
Deblur
You're now ready to denoise your sequences with Deblur. You should pass the sequence length value you selected from the quality score plots for --p-trim-length. This will trim all sequences to this length, and discard any sequences which are not at least this long.
Note: We use a trim length of 250 based on the quality score plots generated from the tutorial data set. Do not use 250 with your own data set, as this value will depend on your data set's read lengths. Use the quality score plots to choose an appropriate trim length for your data.
qiime deblur denoise-16S \
--i-demultiplexed-seqs demux-joined-filtered.qza \
--p-trim-length 250 \
--o-representative-sequences rep-seqs.qza \
--o-table table.qza \
--p-sample-stats \
--o-stats deblur-stats.qza
View summary of Deblur feature table
You can next summarize the feature table resulting from q2-deblur. This table and the corresponding representative sequences are now ready to be analyzed with the same methods and visualizers that would be used on single-end read data.
qiime feature-table summarize \
--i-table table.qza \
--o-visualization table.qzv
Importing pre-joined reads
If you have joined your reads outside of QIIME 2, for example with fastq-join, this section will illustrate how to import those reads. First, download the following demultiplexed and joined read data, which has been joined on a per-sample basis with fastq-join.
Unzip this file as follows:
unzip fj-joined.zip
Import reads
Next, use qiime tools import to import this data. The format that is currently used here is SingleEndFastqManifestPhred33 - this will likely be updated in the future to a format that clearly describes this as joined read data, but in the meantime you should follow the formatting guidelines for the single-end "Fastq Manifest" formats.
qiime tools import \
--input-path fj-joined/manifest \
--output-path fj-joined-demux.qza \
--type SampleData[JoinedSequencesWithQuality] \
--source-format SingleEndFastqManifestPhred33
Viewing summary of imported data with read quality
You can generate a summary of the resulting artifact as follows:
qiime demux summarize \
--i-data fj-joined-demux.qza \
--o-visualization fj-joined-demux.qzv
You can now continue analyses with your joined reads as described above, e.g. quality filtering with q2-quality-filter, denoising with q2-deblur, or dereplicating and picking OTUs with q2-vsearch.
Happy QIIMEing! 
I should have known better than to start just before a new release.