NAME

       unicycler_check - long read assembly checker

SYNOPSIS

       unicycler_check   [-h]   --sam   SAM   --ref   REF   --reads   READS  [--min_len  MIN_LEN]
       [--error_window_size    ERROR_WINDOW_SIZE]     [--depth_window_size     DEPTH_WINDOW_SIZE]
       [--error_rate_threshold ERROR_RATE_THRESHOLD] [--depth_p_val DEPTH_P_VAL] [--window_tables
       WINDOW_TABLES] [--base_tables BASE_TABLES] [--html HTML] [--threads THREADS]  [--verbosity
       VERBOSITY]

DESCRIPTION

       Long read assembly checker

OPTIONS

       -h, --help
              show this help message and exit

       --sam SAM
              Input  SAM  file  of  alignments (if this file doesn't exist, the alignment will be
              performed with results saved to this file - you can use the aligner arguments  with
              this script)

       --ref REF
              FASTA file containing one or more reference sequences

       --reads READS
              FASTQ file of long reads

       --min_len MIN_LEN
              Minimum  alignment  length  (bp)  -  exclude  alignments  shorter  than this length
              (default: 100)

       --error_window_size ERROR_WINDOW_SIZE
              Window size for error summaries (default: 100)

       --depth_window_size DEPTH_WINDOW_SIZE
              Window size for depth summaries (default: 100)

       --error_rate_threshold ERROR_RATE_THRESHOLD
              Threshold for high error rates, expressed as the fraction between  the  mean  error
              rate and the random alignment error rate (default: 0.3)

       --depth_p_val DEPTH_P_VAL
              P-value for low/high depth thresholds (default: 0.001)

       --window_tables WINDOW_TABLES
              Path  and/or  prefix  for  table  files  summarising reference errors for reference
              windows (default: do not save window tables)

       --base_tables BASE_TABLES
              Path and/or prefix for table  files  summarising  reference  errors  at  each  base
              (default: do not save base tables)

       --html HTML
              Path for HTML report (default: do not save HTML report)

       --threads THREADS
              Number of CPU threads used to align (default: the number of available CPUs)

       --verbosity VERBOSITY
              Level of stdout information (0 to 2) (default: 1)

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.