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Filter.shared (version 1.39.5.0)

shared - specify your shared file:

label - OTU Labels:

If none selected, all labels will be output

Select groups for to include in this grouping:

minabund - indicate the minimum abundance required for each sample in a given OTU:

If any samples abundance falls below the minimum, the OTU is removed

minpercent - indicate the minimum relative abundance of an OTU:

For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed

rarepercent - indicate the percentage of otus to remove:

The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance

keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU:

For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10

minnumsamples - indicate the minimum number of samples present in an OTU:

If the number of samples present falls below the minimum, the OTU is removed

minpercentsamples - indicate the minimum percent of sample present in an OTU:

For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, the minimum is 0.50, so the OTU will be removed (Default=0)

mintotal - indicate the minimum abundance required for a given OTU:

If abundance across all samples falls below the minimum, the OTU is removed

makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed:

This will preserve the number of reads in your dataset

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The filter.shared is used to remove OTUs based on various critieria.