unicycler_scrub1

Usage

Overview

Unicycler-scrub - read trimming, chimera detection and misassembly detection

Options

-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)