270    ◾    Bioinformatics

qiime demux emp-single

# EMP-multiplexed single-end reads

qiime demux emp-paired

# EMP-multiplexed paired-end reads

qiime cutadapt demux-single # non-EMP-multiplexed single-end reads

qiime cutadapt demux-paired

# non-EMP-multiplexed paired-end reads

The following is a format for demultiplexing EMP-multiplexing single-end reads. Notice

that the input for the command is an artifact that is created by importing a FASTQ file as

discussed above.

FIGURE 7.3  Demultiplexing plugin for different multiplexed data types.