Classify Long Read Amplicons output

The tool outputs an abundance table. In addition, the following outputs are available in the final wizard step (figure 4.22):

Image createamplicon_output
Figure 4.22: Classify Long Read Amplicons output options.

The Classify Long Read Amplicons abundance table

The abundance table output by Classify Long Read Amplicons contains a list of the identified taxonomies that passed the minimum coverage threshold, and the abundance assigned to each taxonomy. Given the probabilistic nature of the algorithm, the reported abundance is not equivalent to a read count, but rather it represents an estimated abundance. The estimate can contain fractions of reads, but the final reported abundance is rounded to the nearest integer.

In contrast to OTU or ASV abundance tables, Classify Long Read Amplicons abundance tables do not contain a sequence for the taxonomies. This is because the reads are not assigned to a sequence but to a taxonomy. Multiple reference sequences may have the same taxonomy (depending on the provided reference database), so all reads assigned to any of the sequences will count towards the abundance for the taxonomy.

Otherwise, the abundance table contains the same columns, views, and options as the OTU abundance table. See The OTU abundance table for a detailed description of the abundance table options.

The Classify Long Read Amplicons report

An example report can be seen in figure 4.23.

Image createamplicon_report
Figure 4.23: Classify Long Read Amplicons report.

The report contains summary statistics of the results, which can be used for quality checking and verification. It is divided into four sections: