Hail helper functions for the gnomAD project and Translational Genomics Group

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

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

Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

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

PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

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

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

🪛 Fetch ncbi metadata for sra and assemblies

Download genomes from NCBI GenBank FTP site

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

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

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

read data generator

The published study can be accessed on https://www.mdpi.com/1999-4915/12/12/1414

Repository accompanying review in avian genomes by Bravo et al.

The second part of https://github.com/npanuhin/BIOCAD

Randomly download genomes from NCBI RefSeq and Genbank