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Panoramic - a package for eukaryotic pan-genome construction

Quick intro

Panoramic is a software package that construct eukaryotic pan-genomes from scratch. It provides two pipelines implementing two different approaches for pan-genome construction: the "de-novo" approach and the "map-to-pan" 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. This paper provides useful explanations and figures regarding the two 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.

Questions and bug reports

Please submit all your questions to the Issues section of this repository.

Publication and citing

Panormaic has not been published yet. If you use it, please cite the github URL https://github.com/MayroseLab/Panoramic.