[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

Earl Grey: A fully automated TE curation and annotation pipeline

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

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

De novo genome assembly and multisample variant calling

A genome diagram generator for microbes and organelles

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

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