Somatic structural variant caller for long-read data

MEMO: MEM-based pangenome indexing for k-mer queries

Pangenome Mutation-Annotated Networks

Multiple sequence alignment of long tandem repeats

strange pangenome and huge graph visualization

An R package for comparative transcriptomic analyses of hybrids and their progenitors

Animation engine for explanatory math videos

A high-performance BigWig and BigBed library in Rust

Tool for fully-automated inference of species trees from raw genome assemblies

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

Fast and exact gap-affine partial order alignment

cDNA read preprocessing

Lightweight mosaic/somatic SV caller for long reads (WIP)

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

tiara – a tool for DNA sequence classification

deep learning-inspired explainable sequence model for transcription initiation

a precise pangenome browser combining linear and graph-based pan-genome

alignment to variation graph inducer

LongcallR is a small variant caller for single molecule long-read RNA-seq data

a minimal, scriptable genome browser for python

TEtrimmer: a novel tool to automate manual curation of transposable elements

Python wrapper for wavefront alignment using WFA2-lib

Workflow to visualize pggb graphs in jbrowse