NAME

       unicycler_scrub - read trimming, chimera detection and misassembly detection

SYNOPSIS

       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]

DESCRIPTION

       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)

              0 = no stdout,

              1 = basic progress indicators,

              2 = extra info,

              3 = debugging info

SEE ALSO

       unicycler(1)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.