NAME¶

SYNOPSIS¶

DESCRIPTION¶

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¶

AUTHOR¶