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.