.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PILERCR "1" "December 2020" "pilercr 1.06+dfsg" "User Commands"
.SH NAME
pilercr \- software for finding CRISPR repeats
.SH DESCRIPTION
pilercr v1.06
http://www.drive5.com/piler
.SH AUTHOR
Written by Robert C. Edgar
This software is donated to the public domain.
Please visit web site for requested citation.
.SS "Basic options:"
.TP
\fB\-in\fR <filename>
Sequence file to analyze (FASTA format).
.TP
\fB\-out\fR <filename>
Report file name (plain text).
.TP
\fB\-seq\fR <filename>
Save consensus sequences to this FASTA file.
.TP
\fB\-trimseqs\fR
Eliminate similar seqs from \fB\-seq\fR file.
.TP
\fB\-noinfo\fR
Don't write help to report file.
.TP
\fB\-quiet\fR
Don't write progress messages to stderr.
.SS "Criteria for CRISPR detection, defaults in parentheses:"
.TP
\fB\-minarray\fR <N>
Must be at least <n> repeats in array (3).
.TP
\fB\-mincons\fR <F>
Minimum conservation (0.9).
At least N repeats must have identity
>= F with the consensus sequence.
Value is in range 0 .. 1.0.
It is recommended to use a value < 1.0
because using 1.0 may suppress true
arrays due to boundary misidentification.
.TP
\fB\-minrepeat\fR <L>
Minimum repeat length (16).
.TP
\fB\-maxrepeat\fR <L>
Maximum repeat length (64).
.TP
\fB\-minspacer\fR <L>
Minimum spacer length (8).
.TP
\fB\-maxspacer\fR <L>
Maximum spacer length (64).
.TP
\fB\-minrepeatratio\fR <R>
Minimum repeat ratio (0.9).
.TP
\fB\-minspacerratio\fR <R>
Minimum spacer ratio (0.75).
\&'Ratios' are defined as minlength / maxlength,
thus a value close to 1.0 requires lengths to
be similar, 1.0 means identical lengths.
Spacer lengths sometimes vary significantly, so
the default ratio is smaller. As with \fB\-mincons\fR,
using 1.0 is not recommended.
.SS "Parameters for creating local alignments:"
.TP
\fB\-minhitlength\fR <L>
Minimum alignment length (16).
.TP
\fB\-minid\fR <F>
Minimum identity (0.94).