An analysis and visualization platform for 'omics data
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Updated
Aug 31, 2024 - Python
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)
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
An accurate aligner of long reads to a variation graph, based on co-linear chaining
generating hardware accelerators for pangenomic graph queries
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 Analysis in Prokaryotes Lesson
Pangenome Mutation-Annotated Networks
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) 🌾
This repository contains the files from my master thesis project required to conduct a whole-genome analysis of haploblocks in wheat based on pairwise comparisons between assemblies. This is based on a previous method (https://doi.org/10.1038/s42003-020-01413-2), but focuses on the the quality of the pairwise comparisons to call haplotypes.
Library to parse, edit and handle in memory GFA graphs
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