table of contents
| CHIMERASLAYER(1) | User Commands | CHIMERASLAYER(1) |
NAME¶
chimeraslayer - detects likely chimeras in PCR amplified DNA
DESCRIPTION¶
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 utility.
ChimeraSlayer is part of the microbiomeutil suite.
OPTIONS¶
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)
- -R
- min divergence ratio default: 1.007
- -P
- min percent identity among matching sequences (default: 90)
Parameters to tune ChimeraParentSelector:¶
Scoring parameters:
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
SEE ALSO¶
AUTHOR¶
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other distribution.
| June 2013 | chimeraslayer |