lifecn/Pangenome-graph-for-bacterial-pathogens - GitHub
Microbial genomics pipeline to build and analyse genome graphs First version of best practice pipeline for use of graph genomes in microbial genomics, which include Use whole genomes as input for constructing pangenome graph, in which the variation graph data model describes the all versus all alignment of many sequences
A graph-based approach for the visualisation and analysis of bacterial …
2022年10月8日 · Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia.
PanGraph : scalable bacterial pan-genome graph construction
We built pangenome graphs from fully assembled chromosomes from five different bacterial species. For each species we built graphs with three different alignment kernel options ( minimap2 with asm10 or asm20 options and mmseqs2 ) and two different settings for the pseudo-energy parameters α and β (standard or null values).
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
2021年9月14日 · We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs …
Augmenting bacterial similarity measures using a graph-based genome …
2024年6月28日 · In this study, we propose a data scaling method, which adds a novel similarity measure to traditional 16S rRNA distance scores, using matrix transformation. Our pairwise measure is based on a graphical structure of a bacterial genome, using ortholog location to form a numerical representation of synteny.
PanGraph : scalable bacterial pan-genome graph construction
2023年6月6日 · Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments.
Panakeia - a universal tool for bacterial pangenome analysis
2022年4月5日 · The full pangenome graph is the most important output of the Panakeia pipeline, it enables all further analyses steps and visualisation of the data. This graph includes all protein clusters and all local edges for neighborhood connections that occur in more genomes than the given minimal support threshold.
PanGraph : scalable bacterial pan-genome graph construction
We have developed a tool, PanGraph, that can compare the genomes of hundreds of bacteria and summarize them as a graph. This graph represents the large-scale diversity that accumulated in the history of the collection of genomes and is the entry point for further analyses of …
Pasa: leveraging population pangenome graph to scaffold …
2023年12月12日 · A pangenome graph can be built from a set of bacterial genome assemblies by using tools such as Roary , Panaroo or PanTA . The latter can construct the graph progressively by adding new genomes into an existing pangenome.
PanGraph: scalable bacterial pan-genome graph construction
2022年12月13日 · Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as an undirected path along vertices, which in turn, encapsulate homologous multiple sequence alignments.