An analysis and visualization platform for 'omics data
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Federating genomes with love (and synteny derived from functional annotations)
generating hardware accelerators for pangenomic graph queries
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
An accurate aligner of long reads to a variation graph, based on co-linear chaining
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
Optimal sequence-to-graph alignment with recombinations
AMR/VF LGT focused bacterial genomics analysis workflow
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
Construct and Analyze the North American Vitis pangenome
A pipeline for construction and graphical visualization of annotated pangenome networks.
Pangenome Mutation-Annotated Networks
Pangenome Analysis in Prokaryotes Lesson
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Scripts for Hill et al. (in review) 🌾
Extension to the Crop Haplotypes website showing shared haplotypes between wheat genome assemblies. Enables mapping genomic regions of interest to the assemblies and calculate quality parameters such as alignment density or continuity
Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
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