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Perform open-reference OTU picking (version 1.9.1.0)

Input sequence files:

The OTU picking method to use for reference and de novo steps:

Reference sequences to query:

Reference sequences:

Use different reference sequences for the prefilter?:

Unique identifier for OTUs that get created in this ref set:

This is useful to support combining of reference sets

Run in parallel where available?:

Percent of failure sequences to include in the subsample to cluster de novo:

Large numbers should give more comprehensive results but will be slower

Percent of sequence pre-cluster against the reference:

Any reads which fail to hit are discarded (a quality filter)

Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional):

This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus

Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional):

This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus

Minimum number of sequences that must fail to hit the reference for subsampling to be performed:

If fewer than this number of sequences fail to hit the reference, the de novo clustering step will run serially rather than invoking the subsampled open reference approach to improve performance

Suppress the final de novo OTU picking step?:

It may be necessary for extremely large data sets

Minimum otu size to retain the OTU:

Skip the taxonomy assignment step?:

It results in an OTU table without taxonomy

Skip the sequence alignment and tree-building steps?:

What it does

This tool performs open-reference OTU picking from sequences.

This script is broken down into 4 possible OTU picking steps, and 2 steps involving the creation of OTU tables and trees.

More information about this tool is available on QIIME documentation.