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

Long read / genome alignment software

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

Randomly subsample sequencing reads or alignments

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

Earl Grey: A fully automated TE curation and annotation pipeline

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

De novo genome assembly and multisample variant calling

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

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Long-reads Gap-free Chromosome-scale Assembler

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

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

Bioinformatics on GCP, AWS or Azure

A genome diagram generator for microbes and organelles

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

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

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

BRIG is a cross-platform (Windows/Mac/Linux) application that displays circular comparison images of multiple genomes using BLAST.

visual analysis of your VCF files

An Efficient Swiss Army Knife for Population Genomic Analyses in R

A minimal genetic data explorer that processes all genetic information locally.

Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

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

Bacterial surveillance pipeline.

A python project for analysis of codon usage for gene or genome analysis

Development repo for pyani-plus (the next iteration of pyani)

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

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