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| UNICYCLER(1) |
User Commands |
UNICYCLER(1) |
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
- -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.
