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Chimera.check (version 1.39.5.0)

fasta - Candiate Aligned Sequences:

Select Reference Template from:

reference - Reference to align with:

ksize - kmer length to determine differences between sequence fragments:

uses default if < 1

increment - Increment for window slide on each iteration:

Default is 10, but you may set it up to sequence length minus twice the window.

svg - Generate a SVG plot for each query sequence:

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 chimera.check command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.

Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.