eggnog-mapper
ncbi-genome-download
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| eggnog-mapper | ncbi-genome-download | |
|---|---|---|
| 1 | 4 | |
| 529 | 887 | |
| 3.0% | - | |
| 4.3 | 5.7 | |
| about 2 months ago | 9 months ago | |
| Python | Python | |
| GNU Affero General Public License v3.0 | Apache License 2.0 |
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eggnog-mapper
ncbi-genome-download
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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
What are some alternatives?
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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
gisaid-uploader - Simplified & efficient GISAID interactions.
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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