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)