other versions
| 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 |