ncbi-genome-download
clinker
| ncbi-genome-download | clinker | |
|---|---|---|
| 4 | 2 | |
| 891 | 501 | |
| - | - | |
| 5.7 | 3.2 | |
| 10 months ago | 10 months ago | |
| Python | Python | |
| Apache License 2.0 | MIT License |
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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
clinker
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Need help with protein gene-neighborhood methods.
Being a silent reader all this while, this is my first question here and a very basic indeed. I want to generate some gene neighborhood clusters for a set of protein fasta files I have from UniProtKB. I plan to use: 1. http://www.webflags.se/ and 2. https://github.com/gamcil/clinker
- Stuck Running Bioinformatics Tool Through Command
What are some alternatives?
galaxy - Data intensive science for everyone.
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
pyfaidx - Efficient pythonic random access to fasta subsequences
quast - Genome assembly evaluation tool
gisaid-uploader - Simplified & efficient GISAID interactions.
pyGenomeViz - A genome visualization python package for comparative genomics
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report.
Biopython - Official git repository for Biopython (originally converted from CVS)
dash - Data Apps & Dashboards for Python. No JavaScript Required.
UPIMAPI - UniProt Id Mapping through API
scanpy - Single-cell analysis in Python. Scales to >1M cells.