Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

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

Toolbox for Studying Bacteria, Archaea, and Complex Taxons

non-redundant, compressed, journalled, file-based storage for biological sequences

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

Long read / genome alignment software

Earl Grey: A fully automated TE curation and annotation pipeline

De novo genome assembly and multisample variant calling

A Python library for Gene–environment interaction analysis via deep learning

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

Randomly subsample sequencing reads or alignments

provides common tools and lookup tables used primarily by the hgvs and uta packages

Long-reads Gap-free Chromosome-scale Assembler

Scripts and procedures for detecting positively selected genes and codons in primates

Bioinformatics on GCP, AWS or Azure

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

A collaborative notebook for genes and genomes

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.