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

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

Assembled Genomes Compressor

genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.

Hail helper functions for the gnomAD project and Translational Genomics Group

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

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

A modern genomics framework for julia

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

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

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

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

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, directly modify almost all features in Chrome by click the feature

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

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

A mosaic genome painting tool for plant genomes

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

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

Teaching materials for SymbNET course: from MAGs to GEMs

Genome browser to visualize and analyze genomic data

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.

Perl script to download genomes within a clade from NCBI Refseq

:white_circle: :arrow_right: :mag: :information_source: A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

Shiny app that plots NCBI genomes size versus protein count

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

A Genome generation library, for all your genetic algorithmic needs.

Identification of putative duplicated genes among bacterial genomes