266    ◾    Bioinformatics

know that to execute any QIIME2 command, you must use “qiime”. We also mentioned

above that “tools” is a command and command or plugin may have methods or visualizers

or both. The “import” above is a tools command method whose function is to import any

input data. However, for each input file format, different arguments and options will be

used. In general, importing an input file into an artifact will follow this format:

qiime tools import \

--type xxx

#raw data type

--input-path xxx

#the directory

--input-format xxx

#the raw data format

--output-path xxx

#where artifact file is to be saved

The “import” options are self-explanatory, where “--type” specifies the type of the data to

be imported, “--input-path” specifies the path to the raw data files, “--input-format” speci-

fies the input file format, and “--output-path” specifies the path where the artifact file will

be saved.

You must specify the right data type and format on “--type” and “--input-format” for

your input files to be imported successfully.

In the following, we will show you the formats for importing different output files, but

for practice and detailed information, visit “https://docs.qiime2.org/”.

We will discuss the import of the common types of raw data below.

7.3.1.1.1  Importing Raw Data in FASTA

If the raw data is in FASTA format, all sequences must be in a single FASTA file consisting

of exactly two lines for each sequence record; a line for the definition line and a single line

for sequence (not in multiple lines). The ID in each in the definition line must be as per the

FASTA specification (no white space between the “>” and the ID). Moreover, the ID must

follow the “SAMPLEID_SEQID” format, where SAMPLEID is a unique sample identifier

and SEQID is a sequence identifier. Assuming that your sequences are in the “sequences.

fasta” file, you can use the following “qiime tools import” to create an artifact for the input

file:

qiime tools import \

--type ‘FeatureData[Sequence]’ \

--input-path sequences.fna \

--output-path sequences.qza

The above command will import the FASTA sequences as a QIIME2 artifact “sequences.

qza” that is ready for the next step of the analysis.

7.3.1.1.2  Importing EMP-Multiplexed FASTQ Reads

The EMP-multiplexed FASTQ files contain multiplexed reads, but the barcode sequences

are in a separate file. Therefore, there will be two files (forward FASTQ file and barcode

FASTQ file) for single-end reads and three files for paired-end reads (forward, reverse,