.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH UNICYCLER "1" "October 2018" "unicycler 0.4.7" "User Commands"
.SH NAME
unicycler \- assembly pipeline for bacterial genomes
.SH SYNOPSIS
.B unicycler
[\-h] [\-\-help_all] [\-\-version] [\-1 SHORT1] [\-2 SHORT2]
[\-s UNPAIRED] [\-l LONG] \fB\-o\fR OUT [\-\-verbosity VERBOSITY]
[\-\-min_fasta_length MIN_FASTA_LENGTH] [\-\-keep KEEP]
[\-t THREADS] [\-\-mode {conservative,normal,bold}]
[\-\-linear_seqs LINEAR_SEQS] [\-\-vcf]
.SH DESCRIPTION
Unicycler is an assembly pipeline for bacterial genomes. It can assemble
Illumina-only read sets where it functions as a SPAdes-optimiser. It can
also assembly long-read-only sets (PacBio or Nanopore) where it runs a
miniasm+Racon pipeline. For the best possible assemblies, give it both
Illumina reads and long reads, and it will conduct a hybrid assembly.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit
.TP
\fB\-\-help_all\fR
Show a help message with all program options
.TP
\fB\-\-version\fR
Show Unicycler's version number
.SS Input
.TP
\fB\-1\fR SHORT1, \fB\-\-short1\fR SHORT1
FASTQ file of first short reads in each pair
(required)
.TP
\fB\-2\fR SHORT2, \fB\-\-short2\fR SHORT2
FASTQ file of second short reads in each pair
(required)
.TP
\fB\-s\fR UNPAIRED, \fB\-\-unpaired\fR UNPAIRED
FASTQ file of unpaired short reads (optional)
.TP
\fB\-l\fR LONG, \fB\-\-long\fR LONG
FASTQ or FASTA file of long reads (optional)
.SS Output
.TP
\fB\-o\fR OUT, \fB\-\-out\fR OUT
Output directory (required)
.TP
\fB\-\-verbosity\fR VERBOSITY
Level of stdout and log file information (default: 1)
.IP
0 = no stdout,
.IP
1 = basic progress indicators,
.IP
2 = extra info,
.IP
3 = debugging info
.TP
\fB\-\-min_fasta_length\fR MIN_FASTA_LENGTH
Exclude contigs from the FASTA file which are
shorter than this length (default: 100)
.TP
\fB\-\-keep\fR KEEP
Level of file retention (default: 1)
.IP
0 = only keep final files: assembly (FASTA,GFA and log),
.IP
1 = also save graphs at main checkpoints,
.IP
2 = also keep SAM (enables fast rerun in different mode),
.IP
3 = keep all temp files and save all graphs (for debugging)
.TP
\fB\-\-vcf\fR
Produce a VCF by mapping the short reads to the
final assembly (experimental, default: do not
produce a vcf file)
.SS Other
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads used (default: 4)
.TP
\fB\-\-mode\fR {conservative,normal,bold}
Bridging mode (default: normal)
.IP
conservative = smaller contigs, lowest misassembly rate
.IP
normal = moderate contig size and misassembly rate
.IP
bold = longest contigs, higher misassembly rate
.TP
\fB\-\-linear_seqs\fR LINEAR_SEQS
The expected number of linear (i.e. non\-circular)
sequences in the underlying sequence (default: 0)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.