xenial (1) quiver.1.gz

Provided by: pbgenomicconsensus_2.0.0+20151210-1_all bug

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)