DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files) (by Edinburgh-Genome-Foundry)
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers (by kblin)
DnaFeaturesViewer | ncbi-genome-download | |
---|---|---|
2 | 4 | |
547 | 890 | |
2.0% | - | |
5.9 | 5.7 | |
6 months ago | 9 months ago | |
Python | Python | |
MIT License | Apache License 2.0 |
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.
DnaFeaturesViewer
Posts with mentions or reviews of DnaFeaturesViewer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-10.
-
Software to make in-scale illustrations of genomic locations
If you can build a Python environment and do a little coding, DnaFeaturesViewer or pyGenomeViz would be good choices. You can generate the following figure from a Genbank file with about 10 lines of code. Of course, you can specify the range of coordinates to be plotted.
-
pyGenomeViz: A genome visualization python package for comparative genomics
If you need to display annotations/genes within a single genome, DnaFeaturesViewer may be another good option.
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.
-
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
-
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.
-
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
-
Downloading viral genomes programmatically
Useful tool to download from NCBI: ncbi-genome-download
What are some alternatives?
When comparing DnaFeaturesViewer and ncbi-genome-download you can also consider the following projects:
pyGenomeViz - A genome visualization python package for comparative genomics
galaxy - Data intensive science for everyone.
quast - Genome assembly evaluation tool
clinker - Gene cluster comparison figure generator
gggenomes - A grammar of graphics for comparative genomics
pyfaidx - Efficient pythonic random access to fasta subsequences
gisaid-uploader - Simplified & efficient GISAID interactions.
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
DnaFeaturesViewer vs pyGenomeViz
ncbi-genome-download vs galaxy
DnaFeaturesViewer vs quast
ncbi-genome-download vs clinker
DnaFeaturesViewer vs gggenomes
ncbi-genome-download vs pyfaidx
ncbi-genome-download vs gisaid-uploader
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