NAME

       unicycler - assembly pipeline for bacterial genomes

SYNOPSIS

       unicycler [-h] [--help_all] [--version] [-1 SHORT1] [-2 SHORT2] [-s UNPAIRED] [-l LONG] -o
       OUT  [--verbosity  VERBOSITY]  [--min_fasta_length  MIN_FASTA_LENGTH]  [--keep  KEEP]  [-t
       THREADS] [--mode {conservative,normal,bold}] [--linear_seqs LINEAR_SEQS] [--vcf]

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.

OPTIONS

       -h, --help
              Show this help message and exit

       --help_all
              Show a help message with all program options

       --version
              Show Unicycler's version number

   Input
       -1 SHORT1, --short1 SHORT1
              FASTQ file of first short reads in each pair (required)

       -2 SHORT2, --short2 SHORT2
              FASTQ file of second short reads in each pair (required)

       -s UNPAIRED, --unpaired UNPAIRED
              FASTQ file of unpaired short reads (optional)

       -l LONG, --long LONG
              FASTQ or FASTA file of long reads (optional)

   Output
       -o OUT, --out OUT
              Output directory (required)

       --verbosity VERBOSITY
              Level of stdout and log file information (default: 1)

              0 = no stdout,

              1 = basic progress indicators,

              2 = extra info,

              3 = debugging info

       --min_fasta_length MIN_FASTA_LENGTH
              Exclude  contigs  from  the FASTA file which are shorter than this length (default:
              100)

       --keep KEEP
              Level of file retention (default: 1)

              0 = only keep final files: assembly (FASTA,GFA and log),

              1 = also save graphs at main checkpoints,

              2 = also keep SAM (enables fast rerun in different mode),

              3 = keep all temp files and save all graphs (for debugging)

       --vcf  Produce a VCF by mapping the short  reads  to  the  final  assembly  (experimental,
              default: do not produce a vcf file)

   Other
       -t THREADS, --threads THREADS
              Number of threads used (default: 4)

       --mode {conservative,normal,bold}
              Bridging mode (default: normal)

              conservative = smaller contigs, lowest misassembly rate

              normal = moderate contig size and misassembly rate

              bold = longest contigs, higher misassembly rate

       --linear_seqs LINEAR_SEQS
              The  expected  number  of  linear  (i.e.  non-circular) sequences in the underlying
              sequence (default: 0)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.