ncbi

Scripts to download genomes from the NCBI FTP servers

genes and genomes at your fingertips

🐞 Convert NCBI taxonomy dump into lineages

dbSNP

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

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

VAPiD: Viral Annotation and Identification Pipeline

🐣 locally query the ncbi taxonomy

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.

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. 🐵

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

PipeTaxon exposes the ncbi taxonomy database as a REST API.

PLSDB pipeline to collect bacterial plasmids from NCBI

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

Mapping NCBI Genbank accession to GTDB accession

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

A fast, easy way to present complex bioinformatics pipelines to biologists

Subclassification of disease states based on the intersection of literature and expression

An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter

C++ tools for NCBI taxonomy tasks

Make phylogenetic trees and lineages from the NCBI Taxonomy database

Toolkits for NCBI Pubmed

Set of tools for viral metagenomics.

A Rust wrapper around the Entrez API. Helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

Utilities for interacting with NCBI EUtilities relating to PubMed

Utilities for downloading and managing protein FASTA files.