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.

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Rapid determination of appropriate reference genomes.

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Fast and space-efficient taxonomic classification of long reads

F# library for accessing and manipulating bioinformatic datasets.

fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing

Download biological databas, extract database identifier and entrez gene identifier, insert in a mongo database

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

mash works best when given a mash dist file with a bunch of references.

Pipeline for the selection of canonical proteins for reference proteomes

Curated mirror of RefSeq Microbial Genomes. Available via CVMFS repository.

🦇🧫📊Study on bat gut shotgun metagenomics

Downloads plasmids from refseq ftp

GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank.

Mapping RefSeq RNA to OrthoDB (Under Development)

NCBI Genome downloader

Downloading Genomes from RefSeq

Get the latest gene-transcript identifiers using Ensembl, RefSeq, MANE and LRGs models.

Randomly download genomes from NCBI RefSeq and Genbank

Compare the cDNA and protein change nomenclature produced by ANNOVAR and the hgvs/uta python libary for variants downstream of locations where the RefSeq CIGAR string indicates an insertion or deletion difference between the transript and the hg19 sequence.

:arrow_down: Facilitates downloading NCBI's RefSeq with a human-readable file structure

🇨🇭🦠 Service for pathogens and threats identification in hospital environments - SOPHiA Genetics

Batch-resolve NCBI Taxonomy IDs (TaxIDs) from a phyloseq-style taxonomy CSV using Biopython Entrez, with a live tqdm progress bar, caching, resume, safe partial writes, and optional species-rank verification.

Uses 16S to identify a range of possible species.