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Panoramic is a software package that constructs eukaryotic pan-genomes from raw sequencing reads. It provides three pipelines implementing three different approaches for pan-genome construction: the "de-novo" approach, the "map-to-pan" approach, and the 'iterative assembly' approach. In the de-novo pipeline, all input genomes are de-novo assembled and annotated, after which they are compared to one another to create the pan-genome. Gene presence/absence variation (PAV) is detected by means of clustering protein sequences into orthology groups. This is the more "traditional" approach, commonly used for bacterial pan-genomes. The main drawback of this approach is that it requires the full genome annotation of each genome, which is a computationally-intense and challenging process.
The alternative is the map-to-pan approach, in which assembled genomes are first compared to the reference sequence and to one another, through an iterative procedure, to detect "novel" sequences not present in the reference. Annotation is only performed on these novel sequences, thus saving a lot of computations. Gene PAV is detected by mapping sequencing reads to the pan genome sequence and checking the coverage of each gene. The iterative assembly approach is a shortcut, in which reads are first mapped to the reference genome and only unmapped reads are assembled and searched for novel sequences.
This paper provides useful explanations and figures regarding the various approaches. Users may choose one of the approaches, according to their needs and available resources, or they can run both and see which works better for their research. Note that different pipelines often produce rather different results.
Panoramic pipelines take as input a reference genome and annotation as well as reads in FASTQ format (or database identifiers that allow their automatic download). Additional high-quality genome assemblies may be provided, if available. The pipelines result in genome and pan-genome assemblies (in FASTA format), and corresponding annotations (in GFF3 format). In addition, a gene PAV matrix is created and an interactive HTML report is generated.
If you want to try Panoramic, you'll need to set it up first. See the Panoramic setup documentation.
Once setup is complete, you can learn more about configuring and running Panoramic and follow a worked example run.
Please submit all your questions to the Issues section of this repository.
Panoramic (v1.1) was published in MER. If you use it, please cite:
Glick, L., & Mayrose, I. (2021). Panoramic: A package for constructing eukaryotic pan‐genomes. Molecular Ecology Resources