optional arguments:¶

-h, --help

show this help message and exit

--version, -v

show program's version number and exit

--fast5_dir FAST5_DIR, -f FAST5_DIR

Directory containing fast5 files. Can contain multiple subdirectories

--seq_summary_fn SEQ_SUMMARY_FN, -s SEQ_SUMMARY_FN

path of the summary sequencing file where to write the data extracted from the fast5 files

--max_fast5 MAX_FAST5

Maximum number of file to try to parse. 0 to deactivate (default: 0)

--threads THREADS, -t THREADS

Total number of threads to use. 1 thread is used for the reader and 1 for the writer. Minimum 3 (default: 4)

--basecall_id BASECALL_ID

id of the basecalling group. By default leave to 0, but if you perfome multiple basecalling on the same fast5 files, this can be used to indicate the corresponding group (1, 2 ...) (default: 0)

--fields FIELDS [FIELDS ...]

list of field names corresponding to attributes to try to fetch from the fast5 files (default: ['read_id', 'run_id', 'channel', 'start_time', 'sequence_length_template', 'mean_qscore_template', 'calibration_strand_genome_template', 'barcode_arrangement'])

--include_path

If given, the absolute path to the corresponding file is added in an extra column (default: False)

--verbose_level VERBOSE_LEVEL

Level of verbosity, from 2 (Chatty) to 0 (Nothing) (default: 0)