NAME

       bash5tools - Tool for extracting data from .bas.h5 files

SYNOPSIS

       bash5tools   [-h]   [--verbose]   [--version]   [--profile]   [--debug]   [--outFilePrefix
       OUTFILEPREFIX]  [--readType  {ccs,subreads,unrolled}]  [--outType  OUTTYPE]   [--minLength
       MINLENGTH] [--minReadScore MINREADSCORE] [--minPasses MINPASSES] input.bas.h5

OPTIONS

   positional arguments:
       input.bas.h5
              input .bas.h5 filename

   optional arguments:
       -h, --help
              show this help message and exit

       --verbose, -v
              Set the verbosity level (default: None)

       --version
              show program's version number and exit

       --profile
              Print runtime profile at exit (default: False)

       --debug
              Catch exceptions in debugger (requires ipdb) (default: False)

       --outFilePrefix OUTFILEPREFIX
              output filename prefix [None]

       --readType {ccs,subreads,unrolled}
              read type (ccs, subreads, or unrolled) []

       --outType OUTTYPE
              output file type (fasta, fastq) [fasta]

   Read filtering arguments:
       --minLength MINLENGTH
              min read length [0]

       --minReadScore MINREADSCORE
              min read score, valid only with --readType={unrolled,subreads} [0]

       --minPasses MINPASSES
              min number of CCS passes, valid only with --readType=ccs [0]

SEE ALSO

       cmph5tools(1)