[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. `pip install hgvs`

Randomly subsample sequencing reads or alignments

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.

Long-reads Gap-free Chromosome-scale Assembler

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

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

Bioinformatics on GCP, AWS or Azure

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).

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)

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

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

An Efficient Swiss Army Knife for Population Genomic Analyses in R

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

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

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