Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

GENA-LM is a transformer masked language model trained on human DNA sequence.

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Hail helper functions for the gnomAD project and Translational Genomics Group

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

A modern genomics framework for julia

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

A simple command-line tool to download data from Joint Genome Institute databases

The first app for Mobile DNA Sequence Alignment and Analysis

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

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

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

A mosaic genome painting tool for plant genomes

This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

Teaching materials for SymbNET course: from MAGs to GEMs

Genome browser to visualize and analyze genomic data