Galaxy |

Chimera.vsearch (version 1.39.5.2)

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

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

minimum number of differences in segment:

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.vsearch command reads a fasta file and reference file and outputs potentially chimeric sequences.