.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH UNICYCLER_SCRUB "1" "October 2018" "unicycler_scrub 0.4.7" "User Commands"
.SH NAME
unicycler_scrub \- read trimming, chimera detection and misassembly detection
.SH SYNOPSIS
.B unicycler_scrub
[\-h] \fB\-i\fR INPUT \fB\-o\fR OUT [\-r READS] [\-\-trim TRIM]
[\-\-split SPLIT] [\-\-min_split_size MIN_SPLIT_SIZE]
[\-\-discard_chimeras] [\-t THREADS] [\-\-keep_paf]
[\-\-parameters PARAMETERS] [\-\-verbosity VERBOSITY]
.SH DESCRIPTION
Unicycler\-scrub \- read trimming, chimera detection and misassembly detection
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR INPUT, \fB\-\-input\fR INPUT
These are the reads or assembly to be scrubbed (can
be FASTA or FASTQ format
.TP
\fB\-o\fR OUT, \fB\-\-out\fR OUT
The scrubbed reads or assembly will be saved to this
file (will have the same format as the \fB\-\-input\fR file
format) or use "none" to not produce an output file
.TP
\fB\-r\fR READS, \fB\-\-reads\fR READS
These are the reads used to scrub \fB\-\-input\fR (can be
FASTA or FASTQ format) (default: same file as
\fB\-\-input\fR)
.TP
\fB\-\-trim\fR TRIM
The aggressiveness with which the input will be
trimmed (0 to 100, where 0 is no trimming and 100 is
very aggressive trimming) (default: 50)
.TP
\fB\-\-split\fR SPLIT
The aggressiveness with which the input will be
split (0 to 100, where 0 is no splitting and 100 is
very aggressive splitting) (default: 50)
.TP
\fB\-\-min_split_size\fR MIN_SPLIT_SIZE
Parts of split sequences will only be outputted if
they are at least this big (default: 1000)
.TP
\fB\-\-discard_chimeras\fR
If used, chimeric sequences will be discarded
instead of split (default: False)
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads used (default: 4)
.TP
\fB\-\-keep_paf\fR
Save the alignments to file (makes repeated runs
faster because alignments can be loaded from file)
(default: False)
.TP
\fB\-\-parameters\fR PARAMETERS
Low\-level parameters (for debugging use only)
(default: )
.TP
\fB\-\-verbosity\fR VERBOSITY
Level of stdout information (default: 1)
.IP
0 = no stdout,
.IP
1 = basic progress indicators,
.IP
2 = extra info,
.IP
3 = debugging info
.SH SEE ALSO
unicycler(1)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.