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ChimeraSlayer - Online in the Cloud

Run ChimeraSlayer in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command ChimeraSlayer that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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

2. candidate parents of a chimera are selected as those that form a branched best
scoring alignment to the NAST-formatted query sequence

3. the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-
based NAST realignment to the selected reference parent sequences

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

ChimeraSlayer is part of the microbiomeutil suite.


multi-fasta file containing query sequences in alignment format

Common options
db in NAST format (default:

db in fasta format (megablast formatted) (default:

-n number of top matching database sequences to compare to (default 15)

-R min divergence ratio default: 1.007

-P min percent identity among matching sequences (default: 90)

Parameters to tune ChimeraParentSelector:
Scoring parameters:

-M match score (default: +5)

-N mismatch penalty (default: -4)

-Q min query coverage by matching database sequence (default: 70)

-T maximum traverses of the multiple alignment (default: 1)

Parameters to tune ChimeraPhyloChecker
default 50

default 5

minimum bootstrap support for calling chimera (default: 90)

default: 100

(default: 10) If computed BS is between minBS and (minBS - low_range_finer_BS),
then num_finer_BS_replicates computed.

(default: 1000)

-S percent of SNPs to sample on each side of breakpoint for computing bootstrap
support (default: 10)

number of potential parents to test for chimeras (default: 3)

Chimera/Parent alignments with perID above this are considered non-chimeras
(default 100; turned off)

Misc options
shows alignment between query sequence and pair of candidate chimera parents

print ChimeraSlayer alignments in ChimeraSlayer output

chdir to here before running

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