ncbi

There are 211 repositories under ncbi topic.

  • gget

    pachterlab/gget

    🧬 gget enables efficient querying of genomic reference databases

    Language:Python1.1k87277

  • kblin/ncbi-genome-download

    Scripts to download genomes from the NCBI FTP servers

    Language:Python1k34146180

  • ncbi/datasets

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

    Language:Jupyter Notebook4622723553
  • genomepy

    vanheeringen-lab/genomepy

    genes and genomes at your fingertips

    Language:Python386513138

  • pirovc/genome_updater

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

    Language:Shell15924315

  • zyxue/ncbitax2lin

    🐞 Convert NCBI taxonomy dump into lineages

    Language:Python14481830

  • ncbi/dbsnp

    dbSNP

    Language:Jupyter Notebook133231549

  • pirovc/ganon

    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

    Language:Python10247613

  • ncbi/elastic-blast

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

    Language:Python64151718

  • biocommons/eutils

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

    Language:Python59816027

  • rcs333/VAPiD

    VAPiD: Viral Annotation and Identification Pipeline

    Language:Shell5431415

  • hiddenblue/Pubmedsoso

    A Python mini-tool for downloading free PubMed pdf 一个批量下载pubmed免费文献的python小工具

    Language:Python47153

  • pirovc/multitax

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

    Language:Python43464

  • HadrienG/taxadb

    :hatching_chick: locally query the ncbi taxonomy

    Language:Python3932616

  • CCB-SB/plsdb

    PLSDB pipeline to collect bacterial plasmids from NCBI

    Language:Python388324

  • maximilianh/multiSub

    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.

    Language:Python36332

  • Michael-Sebero/Genetic-Trait-Detector

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

    Language:Python36402

  • VascoElbrecht/PrimerMiner

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

    Language:R3664111
  • pmidcite

    dvklopfenstein/pmidcite

    Download "Cited by" data from the NIH for any paper with a PubMed ID

    Language:Python325177

  • suqingdong/pypubmed

    Toolkits for NCBI Pubmed

    Language:Python29158

  • CDCgov/tostadas

    🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

    Language:Python28618315

  • datasnakes/OrthoEvolution

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

    Language:Python283644
  • pipetaxon

    voorloopnul/pipetaxon

    PipeTaxon exposes the ncbi taxonomy database as a REST API.

    Language:Python23354

  • Edinburgh-Genome-Foundry/genome_collector

    :stars: Easily download genomes and build BLAST/Bowtie indexes in Python

    Language:Python2230

  • guyleonard/taxdump_edit

    :seedling: :arrow_right: :deciduous_tree: Add new taxa or taxonomic groups to the NCBI Taxdump files

    Language:Perl20312

  • Jumitti/TFinder

    Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

    Language:Python192717

  • Zenleaf/entrez-rs

    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.

    Language:Rust19323

  • Lattice-Automation/seqparse

    Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format

    Language:TypeScript17354

  • Eslam-Samir-Ragab/Sequence-database-curator

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

    Language:Python15534

  • htafer/remoVecSec

    Module and script to remove contamination in assembled genomes before submission to ncbi

    Language:Python14330

  • medvir/VirMet

    Set of tools for viral metagenomics.

    Language:Python145475

  • NCBI-Hackathons/ATACFlow

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

    Language:Jupyter Notebook149110

  • shenwei356/ncbi_acc2gtdb_acc

    Mapping NCBI Genbank accession to GTDB accession

    1420

  • Picani/fastax

    Make phylogenetic trees and lineages from the NCBI Taxonomy database

    Language:Rust13110

  • pwilmart/fasta_utilities

    Utilities for downloading and managing protein FASTA files.

    Language:Python13417

  • banhbio/Taxonomy.jl

    Julia package to handle the NCBI Taxonomy database.

    Language:Julia12141