---
name: "bash5tools"
section: "1"
platform: "linux"
package: "pbh5tools"
version: "0.8.0+git20170929.58d54ff+dfsg-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/bash5tools"
---

# bash5tools(1)

Tool for extracting data from .bas.h5 files

## 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)](/cmph5tools/1.md)