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.