ncbi

There are 6 repositories under ncbi topic.

kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ncbi bioinformatics download-genomes python biology genomics command-line genbank
Language:Python 893
gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold2 databases enrichment-analysis ensembl gget ncbi reference uniprot alphafold archs4 blast enrichr
Language:Python 867
genomepy
vanheeringen-lab / genomepy
genes and genomes at your fingertips
genome bioconda python ensembl ucsc ncbi
Language:Python 363
ncbi / datasets
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
genomics-data ncbi
Language:Jupyter Notebook 310
pirovc / genome_updater
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
bioinformatics ncbi bash genome sequence refseq genbank download database genomes genomics
Language:Shell 132
zyxue / ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
ncbi-taxonomy taxdump lineage python pandas taxonomy ncbi
Language:Python 129
ncbi / dbsnp
dbSNP
bioinformatics database genomics ncbi variations
Language:Jupyter Notebook 114
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
metagenomics bioinformatics k-mer bloom-filter microbiome minimizers taxonomy genbank gtdb ncbi refseq
Language:Python 80
biocommons / eutils
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
bioinformatics genomics ncbi
Language:Python 55
rcs333 / VAPiD
VAPiD: Viral Annotation and Identification Pipeline
virus annotations genbank bioinformatics virology biology ngs fasta metadata ncbi
Language:Shell 50
ncbi / elastic-blast
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
ncbi blast bioinformatics
Language:Python 39
HadrienG / taxadb
:hatching_chick: locally query the ncbi taxonomy
bioinformatics database ncbi ncbi-taxonomy python taxonomy
Language:Python 37
pirovc / multitax
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
bioinformatics biological-taxonomies greengenes gtdb ncbi open-tree-taxonomy ott pyhton-library python silva taxonomies taxonomy tree
Language:Python 35
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.
sarscov2 sars-cov-2 gisaid-format gisaid-upload gisaid-xls ncbi-ftp genbank tsv ena meta-data fasta gisaid-uploader ncbi
Language:Python 34
CCB-SB / plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
plasmid pipeline ncbi bacteria
Language:Python 31
VascoElbrecht / PrimerMiner
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
metabarcoding bioinformatics primer-design batch-download boldsystems ncbi database-mining
Language:R 30
MichaelSebero / Genetic-Trait-Detector
This python script detects known traits in raw human genetic data.
23andme ancestrydna data detector disease dna gedmatch genetics snp tool snpedia traits genes genotype match allele rsid ncbi mutation offline
Language:Python 29
datasnakes / OrthoEvolution
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
python bioinformatics orthologs biology phylogenetics ncbi ftp blast qsub orthology-inference pbs bash shell genetics sequence-alignment orthology orthologues sge biosql data-science
Language:Python 27
pmidcite
dvklopfenstein / pmidcite
Turbocharge a PubMed literature search using citation counts and data from the NIH
citation-analysis citation-counts citation-downloader citedby command-line-tool library literature-review literature-search ncbi nih-citation-data pmid pubmed snowballing
Language:Python 27
suqingdong / pypubmed
Toolkits for NCBI Pubmed
pubmed ncbi sci
Language:Python 24
pipetaxon
voorloopnul / pipetaxon
PipeTaxon exposes the ncbi taxonomy database as a REST API.
ncbi taxonomy-database ncbi-taxonomy-database api bioinformatics biology computation-biology python django django-rest-framework
Language:Python 23
CDCgov / tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
bioinformatics conda docker liftoff metadata nextflow python vadr scicomp genetics pipeline genbank sequencing sra singularity nf-tower ncbi mpox azure rna-seq
Language:Python 22
Edinburgh-Genome-Foundry / genome_collector
:stars: Easily download genomes and build BLAST/Bowtie indexes in Python
synbio bioinformatics blast python ncbi synthetic-biology taxid bowtie
Language:Python 21
hiddenblue / Pubmedsoso
一个批量下载pubmed免费文献的python小工具
pubmed sci ncbi python scihub spider
Language:Python 17
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.
entrez gene pubmed rust biorust medical bioinformatics ncbi blast
Language:Rust 17
guyleonard / taxdump_edit
:seedling: :arrow_right: :deciduous_tree: Add new taxa or taxonomic groups to the NCBI Taxdump files
taxdump ncbi taxonomy ncbi-taxonomy ncbi-blast ncbi-database ncbi-taxdump
Language:Perl 16
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).
gene fasta database sequence nucleotide protein bioinformatics ncbi fastq redundancy curator genetics genomics metagenomics proteomics
Language:Python 15
NCBI-Hackathons / ATACFlow
An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter
atac-seq beta-release jupyter-notebook ncbi nextflow
Language:Jupyter Notebook 15
htafer / remoVecSec
Module and script to remove contamination in assembled genomes before submission to ncbi
genome assembly ncbi vector contamination vecscreen mitochondria
Language:Python 14
shenwei356 / ncbi_acc2gtdb_acc
Mapping NCBI Genbank accession to GTDB accession
gtdb accession ncbi
14
medvir / VirMet
Set of tools for viral metagenomics.
bioinformatics bioinformatics-pipeline genome miseq python viral-database viral-metagenomics ncbi database bacterial-database
Language:Python 13
Picani / fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
phylogeny phylogenetic-trees bioinformatics-tool command-line-tool rust sqlite sqlite3 ncbi-taxonomy-database ncbi newick
Language:Rust 13
banhbio / Taxonomy.jl
Julia package to handle the NCBI Taxonomy database.
bioinformatics julia phylogeny biodiversity ncbi ncbi-database ncbi-taxonomy taxonomy
Language:Julia 12
NCBI-Hackathons / FlowBio
A fast, easy way to present complex bioinformatics pipelines to biologists
jupyter-notebook ncbi docker nextflow bash pipeline pipeline-framework ngs-pipeline
Language:Shell 12
NCBI-Hackathons / phenotypeXpression
Subclassification of disease states based on the intersection of literature and expression
precision-medicine rna-seq pubmed ncbi-geo ncbi
Language:Python 12
pmenzel / taxonomy-tools
C++ tools for NCBI taxonomy tasks
taxonomy ncbi ncbi-taxonomy
Language:C++ 11

ncbi

kblin / ncbi-genome-download

pachterlab / gget

vanheeringen-lab / genomepy

ncbi / datasets

pirovc / genome_updater

zyxue / ncbitax2lin

ncbi / dbsnp

pirovc / ganon

biocommons / eutils

rcs333 / VAPiD

ncbi / elastic-blast

HadrienG / taxadb

pirovc / multitax

maximilianh / multiSub

CCB-SB / plsdb

VascoElbrecht / PrimerMiner

MichaelSebero / Genetic-Trait-Detector

datasnakes / OrthoEvolution

dvklopfenstein / pmidcite

suqingdong / pypubmed

voorloopnul / pipetaxon

CDCgov / tostadas

Edinburgh-Genome-Foundry / genome_collector

hiddenblue / Pubmedsoso

Zenleaf / entrez-rs

guyleonard / taxdump_edit

Eslam-Samir-Ragab / Sequence-database-curator

NCBI-Hackathons / ATACFlow

htafer / remoVecSec

shenwei356 / ncbi_acc2gtdb_acc

medvir / VirMet

Picani / fastax

banhbio / Taxonomy.jl

NCBI-Hackathons / FlowBio

NCBI-Hackathons / phenotypeXpression

pmenzel / taxonomy-tools