Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Long read / genome alignment software

Randomly subsample sequencing reads

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

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

Earl Grey: A fully automated TE curation and annotation pipeline

De novo genome assembly and multisample variant calling

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

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

Long-reads Gap-free Chromosome-scale Assembler

Bioinformatics on GCP, AWS or Azure

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

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)

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

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 minimal genetic data explorer that processes all genetic information locally.

An Efficient Swiss Army Knife for Population Genomic Analyses in R

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