DOKK / manpages / debian 11 / pycoqc / Fast5_to_seq_summary.1.en
FAST5_TO_SEQ_SUMMARY(1) User Commands FAST5_TO_SEQ_SUMMARY(1)

Fast5_to_seq_summary - generate a sequencing summary like file from a directory containing Fast5 files

usage: Fast5_to_seq_summary [-h] [--version] --fast5_dir FAST5_DIR

[--max_fast5 MAX_FAST5] [--threads THREADS] [--basecall_id BASECALL_ID] [--fields FIELDS [FIELDS ...]] [--include_path] [--verbose_level VERBOSE_LEVEL]

Fast5_to_seq_summary generate a sequencing summary like file from a directory containing Fast5 files

show this help message and exit
show program's version number and exit
Directory containing fast5 files. Can contain multiple subdirectories
path of the summary sequencing file where to write the data extracted from the fast5 files
Maximum number of file to try to parse. 0 to deactivate (default: 0)
Total number of threads to use. 1 thread is used for the reader and 1 for the writer. Minimum 3 (default: 4)
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)
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'])
If given, the absolute path to the corresponding file is added in an extra column (default: False)
Level of verbosity, from 2 (Chatty) to 0 (Nothing) (default: 0)


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

December 2020 Fast5_to_seq_summary 2.5.2