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

BASH5TOOLS(1) User Commands BASH5TOOLS(1)

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)
August 2015 bash5tools 0.8.0