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Chimera.uchime (version 1.39.5.0)

fasta - Candiate Aligned Sequences:

Select Reference Template from:

reference - Reference to align with:

dereplicate - remove chimeric sequences from all groups?:

If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric

skipgaps - columns containing gaps do not count as diffs:

controls how gapped columns affect counting of diffs

skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff:

controls how gapped columns affect counting of diffs

chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format:

Alignments show columns with differences that support or contradict a chimeric model.

minh - mininum score to report chimera. Default 0.3:

Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives.

mindiv - minimum divergence ratio:

to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5

xn - weight of a no vote. Default 8.0:

Decreasing this weight to around 3 or 4 may give better performance on denoised data

dn - pseudo-count prior on number of no votes:

Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4

xa - eight of an abstain vote:

Reasonable values might range from 0.1 to 2.0. Default 1.0

chunks - number of chunks:

number of chunks to extract from the query sequence when searching for parents. Default 4.

minchunk - minimum length of a chunk:

Default 64

maxp - maximum number of candidate parents to consider:

increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. Default 2

minlen - minimum unaligned sequence length:

Applies to both query and reference sequences. Default 10

maxlen - maximum unaligned sequence length:

Applies to both query and reference sequences. Default 10000

idsmoothwindow - the length of id smoothing window:

Default 32

ucl - Use local-X alignments:

global-X is the default

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.uchime command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime

Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options.