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]