Input

1. OTU FASTA file; containing OTU cluster representatives wich have been identified as non-chimeric by the UCHIME tool.
2. File of read sequences in FASTA format, which have been dereplicated by the Dereplicate tool.

Parameters

OTU FASTA file

Of non-chimeric OTU representatives from the 'UCHIME and respectively OTU Cluster' step, this file represents the 'database' to search against.

Input reads file

FASTA file of (dereplicated) reads, these are the query sequences

Minimum identity

Specifies the minimum identity between the query sequence and a database sequence. This is a fractional identity between 0.0 and 1.0. By default set to 0.97, correponding to a minimum identity of 97%.

Output

This tool produces four output files, one of which is hidden by default. To see the hidden file: click on the cogwheel icon in the history panel and select 'Include Hidden Datasets'.

1. A tab delimited file following the rabund format from mothur. The first column is a label (this is usually the identity), the second column is the number of OTUs found and each subsequent column is the number of reads found for the corresponding OTUs.
2. A tab delimited PRE OTU table with three columns: | 1 - OTU label | 2 - Count | 3 - Sequence |

The PRE OTU table can be used as input for the RDP Multi-Classifier to generate a complete OTU table with assigned taxonomy.

3. A FASTA file containing the sequences re-labelled with their corresponding OTU label, e.g. OTU_1, OTU_2,...OTU_N, where N is the number of OTUs