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

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

🐣 locally query the ncbi taxonomy

PLSDB pipeline to collect bacterial plasmids from NCBI

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.

一个批量下载pubmed免费文献的python小工具

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

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

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

Turbocharge a PubMed literature rather than clicking and clicking and clicking on Google Scholar