.TH CHIMERASLAYER "1" "June 2013" "chimeraslayer " "User Commands"
.SH NAME
chimeraslayer \- detects likely chimeras in PCR amplified DNA
.SH DESCRIPTION
ChimeraSlayer is a chimeric sequence detection utility, compatible with
near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
.PP
Chimera Slayer involves the following series of steps that operate to
flag chimeric 16S rRNA sequences:
.IP 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
.IP 2.
candidate parents of a chimera are selected as those that form a
branched best scoring alignment to the NAST-formatted query sequence
.IP 3.
the NAST alignment of the query sequence is improved in a
‘chimera-aware’ profile-based NAST realignment to the selected
reference parent sequences
.IP 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.
.PP
To run Chimera Slayer, you need NAST-formatted sequences generated by
the nast-ier utility.
.PP
ChimeraSlayer is part of the microbiomeutil suite.

.SH OPTIONS
.SS Required
.IP \fB\-\-query_NAST\fR
multi\-fasta file containing query sequences in alignment format
.PP
.SS Common options
.IP \fB\-\-db_NAST\fR
db in NAST format (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta\fP)
.IP \fB\-\-db_FASTA\fR
db in fasta format (megablast formatted) (default: \fI/usr/share/microbiomeutil\-data/RESOURCES/rRNA16S.gold.fasta\fP)
.IP \fB\-n\fR
number of top matching database sequences to compare to (default 15)
.IP \fB\-R\fR
min divergence ratio default: 1.007
.IP \fB\-P\fR
min percent identity among matching sequences (default: 90)
.SS Parameters to tune ChimeraParentSelector:
Scoring parameters:
.IP \fB\-M\fR
match score   (default: +5)
.IP \fB\-N\fR
mismatch penalty  (default: \fB\-4\fR)
.IP \fB\-Q\fR
min query coverage by matching database sequence (default: 70)
.IP \fB\-T\fR
maximum traverses of the multiple alignment  (default: 1)
.SS Parameters to tune ChimeraPhyloChecker
.IP \fB\-\-windowSize\fR
default 50
.IP \fB\-\-windowStep\fR
default 5
.IP \fB\-\-minBS\fR
minimum bootstrap support for calling chimera (default: 90)
.IP \fB\-\-num_BS_replicates\fR
default: 100
.IP \fB\-\-low_range_finer_BS\fR
(default: 10)
If computed BS is between minBS and (minBS \- low_range_finer_BS), then num_finer_BS_replicates computed.
.IP \fB\-\-num_finer_BS_replicates\fR
(default: 1000)
.IP \fB\-S\fR
percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)
.IP \fB\-\-num_parents_test\fR
number of potential parents to test for chimeras (default: 3)
.IP \fB\-\-MAX_CHIMERA_PARENT_PER_ID\fR
Chimera/Parent alignments with perID above this are considered non\-chimeras (default 100; turned off)
.SS Misc options
.IP \fB\-\-printFinalAlignments\fR
shows alignment between query sequence and pair of candidate chimera parents
.IP \fB\-\-printCSalignments\fR
print ChimeraSlayer alignments in ChimeraSlayer output
.IP \fB\-\-exec_dir\fR
chdir to here before running
.SH "SEE ALSO"
http://microbiomeutil.sourceforge.net/#A_CS
.SH AUTHOR
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other
distribution.