AGAT
pyGenomeViz
| AGAT | pyGenomeViz | |
|---|---|---|
| 1 | 3 | |
| 410 | 229 | |
| 3.4% | - | |
| 7.3 | 8.3 | |
| 8 days ago | 7 months ago | |
| Perl | Python | |
| GNU General Public License v3.0 only | MIT License |
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AGAT
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How to download the GTF file for my organism from NCBI? (using featureCounts to obtain gene count data from reads)
There are tools available to convert GFF files to GTF, such as gffread or AGAT.
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
What are some alternatives?
imgui - Dear ImGui: Bloat-free Graphical User interface for C++ with minimal dependencies
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
nwn-lib-d - Library & tools for handling Neverwinter Nights 1/2 resources files
mummer - Mummer alignment tool
pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
gggenomes - A grammar of graphics for comparative genomics
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
FastANI - Fast Whole-Genome Similarity (ANI) Estimation
tinycov - Command line tool to plot genomic coverage from a BAM file
clinker - Gene cluster comparison figure generator
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers