unicycler - assembly pipeline for bacterial genomes

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

unicycler 0.4.7                                   October 2018                                      UNICYCLER(1)

       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.

       unicycler - assembly pipeline for bacterial genomes

-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)

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]