galaxy
ncbi-genome-download
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| galaxy | ncbi-genome-download | |
|---|---|---|
| 4 | 4 | |
| 1,313 | 887 | |
| 2.6% | - | |
| 10.0 | 5.7 | |
| 5 days ago | 9 months ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
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.
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
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?
nextflow - A DSL for data-driven computational pipelines
clinker - Gene cluster comparison figure generator
Biopython - Official git repository for Biopython (originally converted from CVS)
pyfaidx - Efficient pythonic random access to fasta subsequences
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
gisaid-uploader - Simplified & efficient GISAID interactions.
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
galaxy_ng - Ansible Galaxy Server - Issues on https://forum.ansible.com Docs on https://galaxy-ng.readthedocs.io/
UPIMAPI - UniProt Id Mapping through API