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.TH QUIVER 1 "February 2016" "" ""
.SH NAME
quiver \- genomic consensus caller designed for Pacific Biosciences data
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.SH DESCRIPTION
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\fBQuiver\fP 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.
.SS Data file requirements
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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.
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In SMRTportal versions 1.3.3 and prior, by default only a subset of
these quality values are included in the \fB\&.cmp.h5\fP files produced by
SMRTanalysis.  To get a \fB\&.cmp.h5\fP with all the QVs loaded, you will
need to use the \fBRS_Mapping_QVs\fP protocol to create a \fBcmp.h5\fP
file for Quiver.
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If you are using an older version than SMRTportal/SMRTanalysis 1.3.3,
please upgrade.
.SH EXAMPLES
.SS Running Quiver
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For example,
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.nf
.ft C
$ quiver \-j8 aligned_reads.bam              \e
>        \-r path/to/lambda.fasta            \e
>        \-o variants.gff \-o consensus.fasta
.ft P
.fi
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will use 8 CPUs to run Quiver on \fBaligned_reads.bam\fP, outputting
the consensus sequence and variants.
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Note that if you are using a cmp.h5 file and have not used the \fIRS_Mapping_QVs\fP
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.
.SS Run Quiver on Multiple Input Files
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Multiple alignment files in a FOFN (File of File Names) can be quivered against
a single reference (\fIGenomicConsensus\fP >= 1.1.0).
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An example input FOFN:
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.nf
.ft C
$ cat aligned_reads.fofn
/path/to/reads1.bam
/path/to/reads2.bam
.ft P
.fi
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.sp
can be used instead of a reads file:
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.nf
.ft C
$ quiver \-j8 aligned_reads.fofn             \e
>        \-r path/to/lambda.fasta            \e
>        \-o variants.gff \-o consensus.fasta
.ft P
.fi
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.sp
Quiver can also be used with DataSet XML files. See pbcore for details on
generating new DataSet XML files for your alignment files.
.SS Highly\-accurate assembly consensus
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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.
.SH SEE ALSO
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\fBquiver\-faq\fP(7)
\fBplurality\fP(1)
\fBvariantCaller\fP(1)
\fBpbgff\fP(5)
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