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ChimeraSlayer

From mothur

Use Chimera Slayer approach ....

Contents


Algorithm

Default settings

The fasta and template parameters are required. You may enter multiple fasta files by separating them by dashes. Example: fasta=ex.align-abrecovery.align. This method filters columns containing only gap characters.

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

The output to the screen looks like:

Reading sequences and template file... Done.
Processing sequence: 1
Processing sequence: 2
...
Processing sequence: 18

Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093931|MNE12|AF293003	yes
gi|11093925|MNG7|AF292997	yes
gi|11093924|MNF4|AF292996	yes


Opening ex.chimeraslayer.chimeras you would see:

gi|11093941|MNA3|AF293013	yes
parentA: 114709  parentB: 141312
Left Window: 108 5074
Right Window: 5076 6813
Divergence of Query to Leftside ParentA and Rightside ParentB: 0.886896	Bootstrap: 100
Divergence of Query to Rightside ParentA and Leftside ParentB: 1.03588	Bootstrap: 0
Similarity of parents: 74.8436
Similarity of query to parentA: 82.2099
Similarity of query to parentB: 89.0896
DeltaL: -13.5514
DeltaR: 12.4661

gi|11093940|MNF8|AF293012	no
gi|11093939|MNB2|AF293011	no
...

Options

window

The window parameter is used to determine the length of sequence you want in each window analyzed. By default it is set to 100.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=300)
Reading sequences and template file... Done.
Processing sequence: 1
Processing sequence: 2
...
Processing sequence: 18

Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093938|MNC2|AF293010	yes
gi|11093931|MNE12|AF293003	yes
gi|11093930|MNH4|AF293002	yes
gi|11093925|MNG7|AF292997	yes
gi|11093924|MNF4|AF292996	yes

numwanted

The numwanted parameter allows you to specify how many sequences you would each query sequence compared with. By default it is set to 10.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, numwanted=20)
Reading sequences and template file... Done.
Processing sequence: 1
Processing sequence: 2
...
Processing sequence: 18

Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093933|MNA5|AF293005	yes
gi|11093931|MNE12|AF293003	yes
gi|11093927|MND8|AF292999	yes
gi|11093925|MNG7|AF292997	yes

increment

The increment parameter is used to slide the window along the sequence. For the chimeraslayer algorithm the default is 10.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, increment=50)
Reading sequences and template file... Done.
Processing sequence: 1
Processing sequence: 2
...
Processing sequence: 18

Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093938|MNC2|AF293010	yes
gi|11093933|MNA5|AF293005	yes
gi|11093932|MNA1|AF293004	yes
gi|11093931|MNE12|AF293003	yes
gi|11093927|MND8|AF292999	yes
gi|11093924|MNF4|AF292996	yes

ksize

The ksize parameter allows you to input kmersize, default is 7, used if search is kmer.

match & mismatch

The default reward for a match is +5 and the penalty for a mismatch is -4.

divergence

Divergence threshold. The default is 1.007.

minsim

Used to eliminate top matches that don't cover at least this minimum number of the bases in the query sequence, and to eliminate results from parent fragments that do not have this minimum similiarity with the query sequence fragment. The default is 90.

parents

The number of potential parents that are investigated. The default is 3.

iters

The number of iterations performed to get the bootstrapped results. The default is 100.

minsim

The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90.

mincov

The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%.

minbs

The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%.

minsnp

The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)

search

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

processors

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