Search Results - RepositoryStats

ncbi-genome-download kblin

174

957

apache-2.0

35

Scripts to download genomes from the NCBI FTP servers

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

Created 2016-05-03

303 commits to master branch, last one 3 months ago

gget pachterlab

74

951

bsd-2-clause

10

🧬 gget enables efficient querying of genomic reference databases

gget ncbi blast archs4 enrichr ensembl uniprot alphafold databases reference alphafold2 enrichment-analysis

Created 2022-05-04

2,782 commits to main branch, last one a day ago

genomepy vanheeringen-lab

37

382

mit

6

genes and genomes at your fingertips

ncbi ucsc genome python ensembl bioconda

Created 2016-12-16

769 commits to master branch, last one 2 months ago

datasets ncbi

42

374

other

28

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

ncbi genomics-data

Created 2020-04-07

591 commits to master branch, last one 7 days ago

genome_updater pirovc

15

146

mit

1

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

bash ncbi genome refseq genbank genomes database download genomics sequence bioinformatics

Created 2017-05-11

164 commits to master branch, last one 10 months ago

ncbitax2lin zyxue

29

141

mit

8

🐞 Convert NCBI taxonomy dump into lineages

ncbi pandas python lineage taxdump taxonomy ncbi-taxonomy

Created 2016-04-24

92 commits to master branch, last one 2 years ago

dbsnp ncbi

47

127

unknown

26

dbSNP

ncbi database genomics variations bioinformatics

Created 2017-05-08

190 commits to master branch, last one about a year ago

ganon pirovc

13

87

mit

4

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 hierar...

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

Created 2018-08-30

690 commits to master branch, last one 9 months ago

eutils biocommons

25

58

apache-2.0

9

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

ncbi genomics bioinformatics

Created 2016-05-26

268 commits to main branch, last one 5 months ago

VAPiD rcs333

15

51

mit

4

VAPiD: Viral Annotation and Identification Pipeline

ngs ncbi fasta virus biology genbank metadata virology annotations bioinformatics

Created 2016-12-15

355 commits to master branch, last one 3 years ago

elastic-blast ncbi

15

46

other

16

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

ncbi blast bioinformatics

Created 2021-03-31

33 commits to master branch, last one 4 months ago

multitax pirovc

3

40

mit

4

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

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

Created 2021-03-18

77 commits to main branch, last one about a year ago

Pubmedsoso hiddenblue

3

38

unknown

1

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

sci ncbi pubmed python scihub spider

Created 2022-05-11

45 commits to master branch, last one a day ago

multiSub maximilianh

2

35

gpl-3.0

4

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...

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

Created 2021-04-02

74 commits to stable branch, last one 2 years ago

Genetic-Trait-Detector michaelsebero

2

33

gpl-3.0

4

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

Created 2023-02-04

34 commits to main branch, last one 20 days ago