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)