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

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

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

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

Genome browser to visualize and analyze genomic data

Teaching materials for SymbNET course: from MAGs to GEMs