Orographer is in a pre-release status for feedback only. It is currently intended only for use with paraviewer
Orographer reads a BAM file and one or more genomic regions, then generates interactive Bokeh-based HTML plots for reviewing alignments. It supports optional GTF/GFF3 gene tracks and VCF variant overlay. Currently orogapher only supports enhanced visualizations for paraviewer.
Orographer can be installed from source and run on Mac or Linux. It requires a BAM file, reference FASTA, and coordinate(s) in chrom:start-end format. Output is a single-page HTML app with JSON data, suitable for deployment behind a simple HTTP server.
For details, see User Guide.
Plots include:
- Read alignments as arrows with haplotype grouping and strand coloring
- Optional gene track from a bgzip-indexed GTF or GFF3 file
- Optional VCF variant track
- Coordinate navigation (pan, zoom, and a “Go” field to jump to a region)
- Clickable elements for alignment and variant details in a modal
Orographer is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that Orographer lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As Orographer is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any Orographer release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.
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