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.