chimeraslayer − detects likely chimeras in PCR amplified DNA
ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences:
1. |
the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera |
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2. |
candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence |
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3. |
the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences |
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4. |
an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences. |
To run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility.
ChimeraSlayer is part of the microbiomeutil suite.
Required
−−query_NAST
multi−fasta file containing query sequences in alignment format
Common options
−−db_NAST
db in NAST format (default: /usr/share/microbiomeutil−data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)
−−db_FASTA
db in fasta format (megablast formatted) (default: /usr/share/microbiomeutil−data/RESOURCES/rRNA16S.gold.fasta)
−n |
number of top matching database sequences to compare to (default 15) |
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−R |
min divergence ratio default: 1.007 |
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−P |
min percent identity among matching sequences (default: 90) |
Parameters to tune ChimeraParentSelector:
Scoring parameters:
−M |
match score (default: +5) |
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−N |
mismatch penalty (default: −4) |
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−Q |
min query coverage by matching database sequence (default: 70) |
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−T |
maximum traverses of the multiple alignment (default: 1) |
Parameters to tune ChimeraPhyloChecker
−−windowSize
default 50
−−windowStep
default 5
−−minBS
minimum bootstrap support for calling chimera (default: 90)
−−num_BS_replicates
default: 100
−−low_range_finer_BS
(default: 10) If computed BS is between minBS and (minBS − low_range_finer_BS), then num_finer_BS_replicates computed.
−−num_finer_BS_replicates
(default: 1000)
−S |
percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) |
−−num_parents_test
number of potential parents to test for chimeras (default: 3)
−−MAX_CHIMERA_PARENT_PER_ID
Chimera/Parent alignments with perID above this are considered non−chimeras (default 100; turned off)
Misc options
−−printFinalAlignments
shows alignment between query sequence and pair of candidate chimera parents
−−printCSalignments
print ChimeraSlayer alignments in ChimeraSlayer output
−−exec_dir
chdir to here before running
http://microbiomeutil.sourceforge.net/#A_CS
This manual page was written by Andreas Tille <tille AT debian DOT org> but can be freely used for any other distribution.