edgecase
pyGenomeViz
| edgecase | pyGenomeViz | |
|---|---|---|
| 1 | 3 | |
| 15 | 241 | |
| - | - | |
| 2.1 | 7.4 | |
| 5 months ago | 19 days ago | |
| Python | Python | |
| GNU General Public License v3.0 only | MIT License |
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edgecase
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Know a tool that visualizes read sequence extending beyond reference coordinates?
that said, just looking at the raw "show softclipped sequence" in e.g. igv may not be the best scenario either, so creating a custom visualization may be needed anyways. here is another tool i found https://github.com/lankycyril/edgecase from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256856/
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?
ariba - Antimicrobial Resistance Identification By Assembly
mummer - Mummer alignment tool
pipeline-structural-variation - Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
itermplot - An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
pysradb - Package for fetching metadata and downloading data from SRA/ENA/GEO
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
AGAT - Another Gtf/Gff Analysis Toolkit
tinycov - Command line tool to plot genomic coverage from a BAM file
clinker - Gene cluster comparison figure generator