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The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.

Default Settings

The fasta and template parameters are required

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta)

The output to the screen looks like:

Reading sequences from core_set_aligned.imputed.fasta...Done.
Reading sequences from ex.align...Done.
Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093933|MNA5|AF293005	yes
gi|11093927|MND8|AF292999	yes
gi|11093924|MNF4|AF292996	yes
Processing sequence: 18



The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer)

with kmer search you can adjust the ksize, default ksize is 7.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer, ksize=8)


The window parameter allows you to specify the window size for searching for chimeras, default=50.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400)


The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, increment=25)

match & mismatch & numwanted & parents

The match parameter allows you to reward matched bases while selecting potential parents, default is 5. The mismatch parameter allows you to penalize mismatched bases while selecting potential parents, default is -4. The numwanted parameter allows you to specify how many potential parents you would each query sequence compared with, default=15. The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3.

minsim & mincov

The minsim parameter allows you to specify a minimum similarity between the query and the parent fragments, default=90, meaning 90%. The mincov parameter allows you to specify minimum coverage of closest matches found in template and the query. Default is 70, meaning 70%.

iters & minbs & minsnp

The iters parameter allows you to specify the number of bootstrap iters to do, default=100. The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support, default=10, meaning 10%.


The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007.


The processors parameter allows you to specify how many processors you would like to use. The default is 1. If you are using the mpi-enabled version processors is set to the number of processes running.

This command was modeled after the chimeraSlayer written by the Broad Institute.