NAME

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

DESCRIPTION

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

       --seq_summary_fn SEQ_SUMMARY_FN
              [--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

   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)

AUTHOR

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