ncbi

Scripts to download genomes from the NCBI FTP servers

genes and genomes at your fingertips

🐞 Convert NCBI taxonomy dump into lineages

dbSNP

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

🐣 locally query the ncbi taxonomy

VAPiD: Viral Annotation and Identification Pipeline

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. 🐵

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.

PipeTaxon exposes the ncbi taxonomy database as a REST API.

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

PLSDB pipeline to collect bacterial plasmids from NCBI

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

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

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

C++ tools for NCBI taxonomy tasks

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.

Toolkits for NCBI Pubmed

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

Disease Clustering from Literature Based on Minimal Training Data

Utilities for downloading and managing protein FASTA files.

UPWARD: Uniting People Working Against Rare Diseases

NCBI PubMed Crawler

Implements NCBI Contamination Screen Publicly in CWL