---
name: "dextract"
section: "1"
platform: "linux"
package: "dextractor"
version: "1.0-6+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dextract"
---

# dextract(1)

pull information needed for assembly from source HDF5 files made by PacBio RS II sequencer

## NAME

dextract - pull information needed for assembly from source HDF5 files made by PacBio RS II sequencer

## SYNOPSIS

**dextract** \[*-vq*\] \[*-o*\[*\<path\>*\]\] \[*-l\<int(500)\>*\] \[*-s\<int(750)\>*\] *\<input:bax\_h5\>* ...

## DESCRIPTION

Dextract takes a series of .bax.h5 or .subreads.\[bs\]am files as input, and depending on the option flags settings produces:

- 1

  (-f) a.fasta file containing subread sequences, each with a "standard" Pacbio header consisting of the movie name, well number, pulse range, and read quality value.

- 2

  (-a) a FASTA format .arrow file containing the pulse width stream for each subread, with a header that contains the movie name and the 4 channel SNR values.

- 3

  (-q) a FASTAQ-like .quiva file containing for each subread the same header as the .fasta file above, save that it starts with an @-sign, followed by the 5 quality value streams used by Quiver, one per line, where the order of the streams is: deletion QVs, deletion Tags, insertion QVs, merge QVs, and last substitution QVs.

  If the -v option is set then the program reports the processing of each PacBio input file, otherwise it runs silently. If none of the -f, -a, or -q flags is set, then by default -f is assumed. The destination of the extracted information is controlled by the -o parameter as follows:

- 1

  If -o is absent, then for each input file X.bax.h5 or X.subreads.\[bs\]am, dextract will produce X.fasta, X.arrow, and/or X.quiva as per the option flags.

- 2

  If -o is present and followed by a path Y, then the concatenation of the output for the input files is placed in Y.fasta, Y.arrow, and/or Y.quiva as per the option flags.

- 3

  If -o is present but with no following path, then the output is sent to the standard output (to enable a UNIX pipe if desired). In this case only one of the flags -f, -a, or -q can be set.

## SEE ALSO

The full documentation for **dextract:** is maintained as a Texinfo manual.  If the **info** and **dextract:** programs are properly installed at your site, the command

-

  **info dextract**

should give you access to the complete manual.