This is the command quiver that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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