unicycler1
Assembly pipeline for bacterial genomes
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]
Overview
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
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--help_all -
Show a help message with all program options
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--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)
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-s UNPAIRED, --unpaired UNPAIRED -
FASTQ file of unpaired short reads (optional)
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-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)
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0 = no stdout, |
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1 = basic progress indicators, |
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2 = extra info, |
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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)
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0 = only keep final files: assembly (FASTA,GFA and log), |
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1 = also save graphs at main checkpoints, |
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2 = also keep SAM (enables fast rerun in different mode), |
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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)
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conservative = smaller contigs, lowest misassembly rate |
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normal = moderate contig size and misassembly rate |
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bold = longest contigs, higher misassembly rate |
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--linear_seqs LINEAR_SEQS -
The expected number of linear (i.e. non-circular) sequences in the underlying sequence (default: 0)
Releases
Unchanged in 4 releases since Debian 10 (Buster).