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giggles

Genotype Inference using Genome Graphs and Long rEadS (Giggles)

Language:PythonMIT200

SVarp

Phased structural variant discovery in pangenomes

Language:C++MIT2600

MotifScope

A tool for motif annotation and visualization in tandem repeats.

Language:PythonMIT300

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Language:PythonNOASSERTION43700

1000G-ONT-F100-PGGB

PanGenome Graph Building with the first 100 assemblies from the 1000G ONT Sequencing Consortium

Language:RMIT900

Liftoff

An accurate GFF3/GTF lift over pipeline

Language:PythonGPL-3.042000

vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language:C++GPL-3.07000

NAHRwhals

R package and wrapper functions for identifying serial structural variations from genome assemblies

Language:RMIT1600

SVision-pro

Language:PythonGPL-3.02500

agc

Assembled Genomes Compressor

Language:C++MIT15100

kage

Alignment-free genotyper for SNPs and short indels, implemented in Python.

Language:PythonGPL-3.04500

pantas

Differential quantification of alternative splicing events on spliced pangenome graphs

Language:Python500

Severus

A tool for somatic structural variant calling using long reads

Language:PythonNOASSERTION8800

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

Language:R48500

kmerSV

kmerSV: a visualization and annotation tool for structural variants (SVs)

Language:Python800

gpn

Genomic Pre-trained Network

Language:Jupyter NotebookMIT17700

libbdsg

Optimized sequence graph implementations for graph genomics

Language:C++MIT3000

maffer

extract MSAs from genome variation graphs

Language:C++NOASSERTION3300

rs-peanut

GAF alignment evaluation tool.

Language:RustMIT400

vgan

Suite of tools for pangenomics built using vg

Language:C++GPL-3.01700

svtools

Tools for processing and analyzing structural variants.

Language:PythonMIT14300

graphappy

a variation graph-oriented fork of WhatsHap

Language:C++NOASSERTION400

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

Language:RNOASSERTION10500

WFA2-lib

WFA-lib: Wavefront alignment algorithm library v2

Language:CNOASSERTION15600

The-Art-of-Linear-Algebra

Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

Language:PostScriptCC0-1.01707000

wgatools

Whole Genome Alignment Tools

Language:RustMIT9500

somrit

Somatic Retrotransposon Insertion Toolkit

Language:PythonGPL-3.0700

somvarg

Somatic Variants from Graphs

Language:PythonGPL-3.0300

paragraph

Graph realignment tools for structural variants

Language:C++NOASSERTION14800

EVG

A rapid and accurate ensemble pipeline for graph-based variant genotyping with lower depth of short reads

Language:C++MIT2600