pyGenomeViz
ncbi-genome-download
pyGenomeViz | ncbi-genome-download | |
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3 | 4 | |
231 | 893 | |
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8.3 | 5.7 | |
7 months ago | 10 months ago | |
Python | Python | |
MIT License | Apache License 2.0 |
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pyGenomeViz
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How to perform Genome Alignment ?
Do you want to perform a whole genome alignment between species? I often use the following software for genome alignment in prokaryotes and viruses. - MUMmer (pairwise genome Aligner) - progressiveMauve (Multiple Genome Aligner) Due to the high mutation frequency of viral genomes, it is sometimes difficult to compare them at the nucleotide sequence level. Therefore, it may be better to make comparisons at the protein level with MUMmer for viral genomes. I have recently developed the software pyGenomeViz, which automates the process of performing and visualizing whole genome alignments, so check it out if it seems to fit your needs.
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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.
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pyGenomeViz: A genome visualization python package for comparative genomics
GitHub repo: https://github.com/moshi4/pyGenomeViz
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?
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
galaxy - Data intensive science for everyone.
mummer - Mummer alignment tool
clinker - Gene cluster comparison figure generator
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
pyfaidx - Efficient pythonic random access to fasta subsequences
gggenomes - A grammar of graphics for comparative genomics
gisaid-uploader - Simplified & efficient GISAID interactions.
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
Biopython - Official git repository for Biopython (originally converted from CVS)