ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers (by kblin)
gisaid-uploader
Simplified & efficient GISAID interactions. (by greysonlalonde)
| ncbi-genome-download | gisaid-uploader | |
|---|---|---|
| 4 | 1 | |
| 891 | 1 | |
| - | - | |
| 5.7 | 8.7 | |
| 10 months ago | over 2 years ago | |
| Python | Python | |
| Apache License 2.0 | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
ncbi-genome-download
Posts with mentions or reviews of ncbi-genome-download.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-08-02.
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I have a question about the FTP of annotation files from NCBI's Genbank and RefSeq
If you have the taxonomic IDs of your organisms of interest, there are existing parallelized download tools that are more efficient like https://github.com/kblin/ncbi-genome-download or bit-dl-ncbi-assemblies from https://github.com/AstrobioMike/bit
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Bioinformatics without a lab
Downloading from NCBI can be pretty wonky though, but third parties have made good programs to deal with. As an example - and a personal favorite - you have https://github.com/kblin/ncbi-genome-download which by far is the easiest way to download various assembled genomes.
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Downloading genomes from database via command line FTP
I know you said Ensembl, but if you can live with NCBI, I would suggest https://github.com/kblin/ncbi-genome-download
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Downloading viral genomes programmatically
Useful tool to download from NCBI: ncbi-genome-download
gisaid-uploader
Posts with mentions or reviews of gisaid-uploader.
We have used some of these posts to build our list of alternatives
and similar projects.
What are some alternatives?
When comparing ncbi-genome-download and gisaid-uploader you can also consider the following projects:
galaxy - Data intensive science for everyone.
goatools - Python library to handle Gene Ontology (GO) terms
clinker - Gene cluster comparison figure generator
Hail - Cloud-native genomic dataframes and batch computing
pyfaidx - Efficient pythonic random access to fasta subsequences
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
Biopython - Official git repository for Biopython (originally converted from CVS)
UPIMAPI - UniProt Id Mapping through API
eggnog-mapper - Fast genome-wide functional annotation through orthology assignment
bit - Bioinformatics Tools
pyGenomeViz - A genome visualization python package for comparative genomics
ncbi-genome-download vs galaxy
gisaid-uploader vs goatools
ncbi-genome-download vs clinker
gisaid-uploader vs Hail
ncbi-genome-download vs pyfaidx
ncbi-genome-download vs OpenWorm
ncbi-genome-download vs Biopython
ncbi-genome-download vs UPIMAPI
ncbi-genome-download vs eggnog-mapper
ncbi-genome-download vs bit
ncbi-genome-download vs goatools
ncbi-genome-download vs pyGenomeViz