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Chimera.slayer

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The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences. The chimera.slayer command parameters are fasta, template, filter, mask, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted. The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. The processors parameter allows you to specify how many processors you would like to use. The default is 1.

The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. The window parameter allows you to specify the window size for searching for chimeras, default=50. The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5. The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15. The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. The match parameter allows you to reward matched bases in blast search, default is 5. 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. The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100. The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. 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) The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance.

chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta) chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer) chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=blast) chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400) chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, numwanted=10, processors=2)

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