unicycler_scrub - read trimming, chimera detection and misassembly
detection
unicycler_scrub [-h] -i INPUT -o OUT [-r
READS] [--trim TRIM] [--split SPLIT] [--min_split_size MIN_SPLIT_SIZE]
[--discard_chimeras] [-t THREADS] [--keep_paf] [--parameters PARAMETERS]
[--verbosity VERBOSITY]
Unicycler-scrub - read trimming, chimera detection and misassembly
detection
- -h, --help
- show this help message and exit
- -i INPUT, --input
INPUT
- These are the reads or assembly to be scrubbed (can be FASTA or FASTQ
format
- -o OUT, --out
OUT
- The scrubbed reads or assembly will be saved to this file (will have the
same format as the --input file format) or use "none" to
not produce an output file
- -r READS, --reads
READS
- These are the reads used to scrub --input (can be FASTA or FASTQ
format) (default: same file as --input)
- --trim TRIM
- The aggressiveness with which the input will be trimmed (0 to 100, where 0
is no trimming and 100 is very aggressive trimming) (default: 50)
- --split
SPLIT
- The aggressiveness with which the input will be split (0 to 100, where 0
is no splitting and 100 is very aggressive splitting) (default: 50)
- --min_split_size
MIN_SPLIT_SIZE
- Parts of split sequences will only be outputted if they are at least this
big (default: 1000)
- --discard_chimeras
- If used, chimeric sequences will be discarded instead of split (default:
False)
- -t THREADS, --threads
THREADS
- Number of threads used (default: 4)
- --keep_paf
- Save the alignments to file (makes repeated runs faster because alignments
can be loaded from file) (default: False)
- --parameters
PARAMETERS
- Low-level parameters (for debugging use only) (default: )
- --verbosity
VERBOSITY
- Level of stdout information (default: 1)
- 0 = no stdout,
- 1 = basic progress indicators,
- 2 = extra info,
- 3 = debugging info
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.