NAME

       quiver - genomic consensus caller designed for Pacific Biosciences data

DESCRIPTION

       Quiver  is  an algorithm for calling highly accurate consensus from multiple PacBio reads,
       using a pair-HMM exploiting both the basecalls and QV metrics to infer the true underlying
       DNA sequence.

   Data file requirements
       To  make  the  most  accurate  consensus  calls possible, Quiver makes use of a battery of
       quality value metrics calculated by  the  basecaller.   If  you  are  using  a  SMRTportal
       installation  verision  1.4 or later, then SMRTportal will load all the information Quiver
       needs, so you can skip the rest of this section.

       In SMRTportal versions 1.3.3 and prior, by default only a subset of these  quality  values
       are included in the .cmp.h5 files produced by SMRTanalysis.  To get a .cmp.h5 with all the
       QVs loaded, you will need to use the RS_Mapping_QVs protocol to create a cmp.h5  file  for
       Quiver.

       If you are using an older version than SMRTportal/SMRTanalysis 1.3.3, please upgrade.

EXAMPLES

   Running Quiver
       For example,

          $ quiver -j8 aligned_reads.bam              \
          >        -r path/to/lambda.fasta            \
          >        -o variants.gff -o consensus.fasta

       will  use 8 CPUs to run Quiver on aligned_reads.bam, outputting the consensus sequence and
       variants.

       Note that if you are using a cmp.h5 file and have not used the RS_Mapping_QVs protocol  to
       generate  that  file---or  if the source bas.h5 file was generated by pre-1.3.1 instrument
       software---the cmp.h5 will not contain the full battery of QV metrics required for optimal
       Quiver  accuracy.   The  command  will  still  work,  but  it will give a warning that its
       accuracy will be suboptimal.

   Run Quiver on Multiple Input Files
       Multiple alignment files in a FOFN (File of File Names) can be quivered against  a  single
       reference (GenomicConsensus >= 1.1.0).

       An example input FOFN:

          $ cat aligned_reads.fofn
          /path/to/reads1.bam
          /path/to/reads2.bam

       can be used instead of a reads file:

          $ quiver -j8 aligned_reads.fofn             \
          >        -r path/to/lambda.fasta            \
          >        -o variants.gff -o consensus.fasta

       Quiver  can  also be used with DataSet XML files. See pbcore for details on generating new
       DataSet XML files for your alignment files.

   Highly-accurate assembly consensus
       Quiver enables consensus accuracies on genome assemblies at accuracies approaching or even
       exceeding  Q60  (one  error  per million bases).  If you use the HGAP assembly protocol in
       SMRTportal 2.0 or later, Quiver runs automatically as the final "assembly polishing" step.

SEE ALSO

       quiver-faq(7) plurality(1) variantCaller(1) pbgff(5)

                                          February 2016                                 QUIVER(1)