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pachterlab /gget

🧬 gget enables efficient querying of genomic reference databases

rna-seq genomics reference databases ensembl proteomics blast transcriptomics uniprot ncbi enrichment-analysis enrichr alphafold gget archs4 alphafold2

UpdatedMar 15, 2025
Python

kblin /ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

python bioinformatics genomics command-line biology genbank ncbi download-genomes

UpdatedAug 6, 2024
Python

ncbi /datasets

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

ncbi genomics-data

UpdatedMar 12, 2025
Jupyter Notebook

genomepy

vanheeringen-lab /genomepy

genes and genomes at your fingertips

python genome ensembl bioconda ucsc ncbi

UpdatedFeb 21, 2025
Python

pirovc /genome_updater

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

bash bioinformatics database genomics genome download genbank sequence ncbi genomes refseq

UpdatedDec 15, 2024
Shell

zyxue /ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

python taxonomy pandas ncbi-taxonomy ncbi lineage taxdump

UpdatedApr 4, 2022
Python

ncbi /dbsnp

dbSNP

bioinformatics database genomics variations ncbi

UpdatedJun 21, 2024
Jupyter Notebook

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

bioinformatics taxonomy bloom-filter metagenomics genbank microbiome k-mer ncbi refseq minimizers gtdb

UpdatedFeb 12, 2024
Python

biocommons /eutils

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

bioinformatics genomics ncbi

UpdatedJun 26, 2024
Python

rcs333 /VAPiD

VAPiD: Viral Annotation and Identification Pipeline

metadata bioinformatics virus biology annotations ngs genbank fasta ncbi virology

UpdatedMay 29, 2024
Shell

ncbi /elastic-blast

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

bioinformatics blast ncbi

UpdatedJan 13, 2025
Python

pirovc /multitax

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

python taxonomies tree bioinformatics taxonomy ncbi ott silva greengenes gtdb pyhton-library open-tree-taxonomy biological-taxonomies

UpdatedSep 6, 2024
Python

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

python science pdf research tools paper pubmed ncbi sci scihub

UpdatedDec 18, 2024
Python

HadrienG /taxadb

🐣 locally query the ncbi taxonomy

python bioinformatics database taxonomy ncbi-taxonomy ncbi

UpdatedDec 8, 2022
Python

CCB-SB /plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI

pipeline bacteria ncbi plasmid

UpdatedOct 23, 2024
Python

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.

tsv genbank fasta ncbi meta-data ena sars-cov-2 sarscov2 gisaid-uploader gisaid-format gisaid-upload gisaid-xls ncbi-ftp

UpdatedMay 1, 2022
Python

Michael-Sebero /Genetic-Trait-Detector

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

data offline genetics tool match mutation detector dna snp genes disease snpedia traits ncbi genotype 23andme ancestrydna gedmatch allele rsid

UpdatedMar 1, 2025
Python

VascoElbrecht /PrimerMiner

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

bioinformatics ncbi metabarcoding batch-download primer-design boldsystems database-mining

UpdatedOct 30, 2024
R

pmidcite

dvklopfenstein /pmidcite

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

library pubmed command-line-tool pmid ncbi literature-review citation-analysis citation-downloader literature-search citation-counts snowballing nih-citation-data citedby

UpdatedSep 30, 2024
Python

datasnakes /OrthoEvolution

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

python shell bash data-science bioinformatics genetics biology ftp sge phylogenetics blast orthologues qsub orthology-inference ncbi sequence-alignment pbs orthologs orthology biosql

UpdatedDec 8, 2024
Python

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