table of contents
| PILERCR(1) | User Commands | PILERCR(1) |
NAME¶
pilercr - software for finding CRISPR repeats
DESCRIPTION¶
pilercr v1.06 http://www.drive5.com/piler
AUTHOR¶
Written by Robert C. Edgar This software is donated to the public domain. Please visit web site for requested citation.
Basic options:¶
- -in <filename>
- Sequence file to analyze (FASTA format).
- -out <filename>
- Report file name (plain text).
- -seq <filename>
- Save consensus sequences to this FASTA file.
- -trimseqs
- Eliminate similar seqs from -seq file.
- -noinfo
- Don't write help to report file.
- -quiet
- Don't write progress messages to stderr.
Criteria for CRISPR detection, defaults in parentheses:¶
- -minarray <N>
- Must be at least <n> repeats in array (3).
- -mincons <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.
- -minrepeat <L>
- Minimum repeat length (16).
- -maxrepeat <L>
- Maximum repeat length (64).
- -minspacer <L>
- Minimum spacer length (8).
- -maxspacer <L>
- Maximum spacer length (64).
- -minrepeatratio <R>
- Minimum repeat ratio (0.9).
- -minspacerratio <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 -mincons, using 1.0 is not recommended.
Parameters for creating local alignments:¶
- -minhitlength <L>
- Minimum alignment length (16).
- -minid <F>
- Minimum identity (0.94).
| December 2020 | pilercr 1.06+dfsg |