Unicycler

usage: 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]

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Unicycler: an assembly pipeline for bacterial genomes

Help:
  -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: 8)
  --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)