Scripts to download genomes from the NCBI FTP servers

🧬 gget enables efficient querying of genomic reference databases

genes and genomes at your fingertips

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

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

🐞 Convert NCBI taxonomy dump into lineages

dbSNP

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

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

VAPiD: Viral Annotation and Identification Pipeline

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

🐣 locally query the ncbi taxonomy

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

PLSDB pipeline to collect bacterial plasmids from NCBI

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

This python script detects known traits in raw human genetic data.

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Turbocharge a PubMed literature search using citation counts and data from the NIH

Toolkits for NCBI Pubmed