The chimera.vsearch command reads a fasta file and reference file or a fasta and name or count file and outputs potentially chimeric sequences. The vsearch program is donated to the public domain,

Default Settings

The fasta parameter is required.

mothur > chimera.vsearch(fasta=stool.trim.unique.good.align,


mothur > chimera.vsearch(fasta=fasta=stool.trim.unique.good.align, name=fasta=stool.trim.unique.good.names)


mothur > chimera.vsearch(fasta=fasta=stool.trim.unique.good.align, name=fasta=stool.trim.unique.good.names, group=stool.trim.unique.good.groups)

The chimeras file format is explained here.



The vsearch parameter allows you to specify the name and location of your vsearch executable. By default mothur will look in your path and mothur’s executable location. You can set the vsearch location as follows: vsearch=/usr/bin/vsearch.

mothur > chimera.vsearch(vsearch=/usr/bin/vsearch.2.11.1,  fasta=stool.trim.unique.good.align, name=stool.trim.good.names)


You can provide a name file to check for chimeras using more abundant sequences as the reference.

mothur > chimera.vsearch(fasta=stool.trim.unique.good.align, name=stool.trim.good.names)


If you are using reference=self and provide a groupfile, mothur will use the more abundant sequences from the same sample to check the query sequence.

mothur > chimera.vsearch(fasta=stool.trim.unique.good.align, name=stool.trim.good.names, group=stool.good.groups)


The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. The count file can also contain group information.

mothur > make.table(name=stool.trim.good.names, group=stool.good.groups)
mothur > chimera.vsearch(fasta=stool.trim.unique.good.align, count=stool.trim.good.count_table)


The processors parameter allows you to specify how many processors you would like to use. The default is all available.


The dereplicate parameter can be used when checking for chimeras by group. If the dereplicate parameter is false, then if one group finds the sequence to be chimeric, then all groups find it to be chimeric, default=f. If you set dereplicate=t, and then when a sequence is found to be chimeric it is removed from it’s group, not the entire dataset.

Note: When you set dereplicate=t, mothur generates a new count table with the chimeras removed and counts adjusted by sample.


The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).


The chimealns parameter allows you to indicate you would like 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.


The minh parameter - 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. If you decrease xn you may need to increase minh, and vice versa.


The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don’t care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.


The mindiffs parameter - minimum number of differences in segment Default = (3).


The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.


The dn parameter - pseudo-count prior on number of no votes. Default

1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.


  • 1.38.0 First Introduced
  • 1.39.0 Adds chimera.vsearch for Windows users
  • 1.39.2 Bug Fix: removing last character of sequence names when processing with a reference. Not an issue with denovo method.
  • 1.40.0 Fixes screen output. #309
  • 1.42.0 Updates vsearch version to 2.11.1 #585
  • 1.42.0 Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586
  • 1.44.0 Adds parallelization to chimera.vsearch when using denovo method. #700
  • 1.45.0 Adds multiple processors for chimera.vsearch when using reference instead of denovo. #757
  • 1.45.0 Updates vsearch to 2.16.0.