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]