.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH UNICYCLER_CHECK "1" "October 2018" "unicycler_check 0.4.7" "User Commands"
.SH NAME
unicycler_check \- long read assembly checker
.SH SYNOPSIS
.B unicycler_check
[\-h] \fB\-\-sam\fR SAM \fB\-\-ref\fR REF \fB\-\-reads\fR READS
[\-\-min_len MIN_LEN]
[\-\-error_window_size ERROR_WINDOW_SIZE]
[\-\-depth_window_size DEPTH_WINDOW_SIZE]
[\-\-error_rate_threshold ERROR_RATE_THRESHOLD]
[\-\-depth_p_val DEPTH_P_VAL]
[\-\-window_tables WINDOW_TABLES]
[\-\-base_tables BASE_TABLES] [\-\-html HTML]
[\-\-threads THREADS] [\-\-verbosity VERBOSITY]
.SH DESCRIPTION
Long read assembly checker
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-sam\fR SAM
Input SAM file of alignments (if this file doesn't
exist, the alignment will be performed with results
saved to this file \- you can use the aligner
arguments with this script)
.TP
\fB\-\-ref\fR REF
FASTA file containing one or more reference
sequences
.TP
\fB\-\-reads\fR READS
FASTQ file of long reads
.TP
\fB\-\-min_len\fR MIN_LEN
Minimum alignment length (bp) \- exclude alignments
shorter than this length (default: 100)
.TP
\fB\-\-error_window_size\fR ERROR_WINDOW_SIZE
Window size for error summaries (default: 100)
.TP
\fB\-\-depth_window_size\fR DEPTH_WINDOW_SIZE
Window size for depth summaries (default: 100)
.TP
\fB\-\-error_rate_threshold\fR ERROR_RATE_THRESHOLD
Threshold for high error rates, expressed as the
fraction between the mean error rate and the random
alignment error rate (default: 0.3)
.TP
\fB\-\-depth_p_val\fR DEPTH_P_VAL
P\-value for low/high depth thresholds (default:
0.001)
.TP
\fB\-\-window_tables\fR WINDOW_TABLES
Path and/or prefix for table files summarising
reference errors for reference windows (default: do
not save window tables)
.TP
\fB\-\-base_tables\fR BASE_TABLES
Path and/or prefix for table files summarising
reference errors at each base (default: do not save
base tables)
.TP
\fB\-\-html\fR HTML
Path for HTML report (default: do not save HTML
report)
.TP
\fB\-\-threads\fR THREADS
Number of CPU threads used to align (default: the
number of available CPUs)
.TP
\fB\-\-verbosity\fR VERBOSITY
Level of stdout information (0 to 2) (default: 1)
.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.