.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH UNICYCLER_ALIGN "1" "October 2018" "unicycler_align 0.4.7" "User Commands"
.SH NAME
unicycler_align \- sensitive semi-global long read aligner
.SH SYNOPSIS
.B unicycler_align
[\-h] \fB\-\-ref\fR REF \fB\-\-reads\fR READS \fB\-\-sam\fR SAM
[\-\-contamination CONTAMINATION] [\-\-scores SCORES]
[\-\-low_score LOW_SCORE] [\-\-keep_bad]
[\-\-sensitivity SENSITIVITY] [\-\-threads THREADS]
[\-\-verbosity VERBOSITY] [\-\-min_len MIN_LEN]
[\-\-allowed_overlap ALLOWED_OVERLAP]
.SH DESCRIPTION
Unicycler align \- a sensitive semi\-global long read aligner
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-ref\fR REF
FASTA file containing one or more reference
sequences
.TP
\fB\-\-reads\fR READS
FASTQ or FASTA file of long reads
.TP
\fB\-\-sam\fR SAM
SAM file of resulting alignments
.TP
\fB\-\-contamination\fR CONTAMINATION
FASTA file of known contamination in long reads
.TP
\fB\-\-scores\fR SCORES
Comma\-delimited string of alignment scores: match,
mismatch, gap open, gap extend (default: 3,\-6,\-5,\-2)
.TP
\fB\-\-low_score\fR LOW_SCORE
Score threshold \- alignments below this are
considered poor (default: set threshold
automatically)
.TP
\fB\-\-keep_bad\fR
Include alignments in the results even if they are
below the low score threshold (default: low\-scoring
alignments are discarded)
.TP
\fB\-\-sensitivity\fR SENSITIVITY
A number from 0 (least sensitive) to 3 (most
sensitive) (default: 0)
.TP
\fB\-\-threads\fR THREADS
Number of threads used (default: number of CPUs, up
to 8)
.TP
\fB\-\-verbosity\fR VERBOSITY
Level of stdout information (0 to 4) (default: 1)
.TP
\fB\-\-min_len\fR MIN_LEN
Minimum alignment length (bp) \- exclude alignments
shorter than this length (default: 100)
.TP
\fB\-\-allowed_overlap\fR ALLOWED_OVERLAP
Allow this much overlap between alignments in a
single read (default: 100)
.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.