ncbi-genome-download
galaxy
| ncbi-genome-download | galaxy | |
|---|---|---|
| 4 | 4 | |
| 891 | 1,315 | |
| - | 1.4% | |
| 5.7 | 10.0 | |
| 10 months ago | 3 days ago | |
| Python | Python | |
| Apache License 2.0 | GNU General Public License v3.0 or later |
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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
galaxy
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Need for GUIs for bioinformatic tools?
Maybe it would help you to look at the galaxy project: GitHub main site
- BIOINFORMATICS PROJECT
- Any bioinfo open source projects looking for contributors?
- Developed a new kind of dual extruder system on fully custom built 3D printer
What are some alternatives?
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Biopython - Official git repository for Biopython (originally converted from CVS)
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
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
UPIMAPI - UniProt Id Mapping through API
galaxy_ng - Ansible Galaxy Server - Issues on https://forum.ansible.com Docs on https://galaxy-ng.readthedocs.io/