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.

unicycler_check 0.4.7                             October 2018                                UNICYCLER_CHECK(1)