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]