Constructing a pangenome gene graph

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

oxford dot plots

A tool for recovering synteny blocks from multiple alignment

R package for comparison of synteny conservation at the genome-wide scale.

Any Way to Show Multi genomic Synteny

Multi-genome synteny block visualization tool

Detecting multi-genome synteny using minimizer graph mapping

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

Tool Shed repositories maintained by the Intergalactic Utilities Commission

Yet another Hi-C scaffolding tool

Foreign Contamination Screening - GX source code

Draw a dot plot from a paf alignment

Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters

TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments

base-accurate DNA sequence alignments using WFA and mashmap3

Pairwise whole genome aligner

Fast Tandem Repeat Finder

Portable solution to generate genome alignment chains using lastz

BUSCO_Phylogenomics | Pipeline to construct species phylogenies using BUSCO proteins

Fast genomics quality control tools for sequencing data, written in Rust.

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

Evaluate variant calls and its combination with k-mer multiplicity

lumpy: a general probabilistic framework for structural variant discovery

Genome Interval Arithmetic in R

Collection of low-level functions for working with vctrs

Tidy Plots for Scientific Papers

The web framework for content-driven websites. ⭐️ Star to support our work!

Finding Recurrent Substitutions in Multiple Sequence Alignments

Tool for drawing gene structures from genome annotation files.