This is the command bash5tools that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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]
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