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Filter OTUs from an OTU table (version 1.9.1.0)

Input OTU table:

The input otu table filepath in biom format

Minimum total observation count of an otu for that otu to be retained:

Fraction of the total observation (sequence) count to apply as the minimum total observation count of an otu for that otu to be retained:

This is a fraction (float), not a percentage, so if you want to filter to 1%, you need to use 0.01 as value here

Maximum total observation count of an otu for that otu to be retained:

Minimum number of samples an OTU must be observed in for that otu to be retained:

Maximum number of samples an OTU must be observed in for that otu to be retained:

Do you want to exclude a predefined list of OTUs from the OTU table?:

What it does

The Qiime script filter_otus_from_otu_table.py filter OTUs from an OTU table based on their observation counts or identifier.

Different kind of filtering can be applied on the input biom file depending on the selected parameters:

Singleton filtering (minimum number of occurence) by using the -n/--min_count parameters
Abundance filtering (maximum number of occurence) by using the -x/--max_count parameters
Chimera filtering by using the -e/--otu_ids_to_exclude_fp parameters

More information about this tool is available on QIIME documentation.