megahit
nanopolish
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| megahit | nanopolish | |
|---|---|---|
| 1 | 1 | |
| 558 | 541 | |
| - | - | |
| 0.0 | 5.2 | |
| 25 days ago | 9 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 only | MIT License |
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.
megahit
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Woman has had her twitter blocked after proving that the covid-19 vaccine has been created from a computer generated genomic sequence of the virus & not one isolated from an infected person
If you read carefully, you will find that they used the expected genome to find the genome in their cell culture. They used RT-PCR at 40 cycles to magnify the sequences of the published genome, then used a software library (https://github.com/voutcn/megahit) to assemble into a full sequence. So in other words, they had a soup of a lot of things, they saw cytopathic effects which they attribute to the virus replicating (even though it could easily be attributed to the chemicals that they used in their cocktail), then they extracted the DNA they expected to find using RT-PCR. This is not an isolate, they didnt isolate something, measure it, and find it matches the published DNA. They cultured and extracted the information they expected to find. It is circular reasoning.
nanopolish
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ONT Frustration
I use nanopore for de novo methylation motif detection and some ssDNA signal comparison. Tombo has not worked with R10 data for me, so I’ll have to revisit that. Nanocompore uses Nanopolish for signal comparison, which does not support R10 data (see github).
What are some alternatives?
bowtie2 - A fast and sensitive gapped read aligner
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
hap.py - Haplotype VCF comparison tools
bowtie - An ultrafast memory-efficient short read aligner
bwa-mem2 - The next version of bwa-mem
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
seq - A high-performance, Pythonic language for bioinformatics
opensim-core - SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
octopus - Bayesian haplotype-based mutation calling
stellarium - Stellarium is a free GPL software which renders realistic skies in real time with OpenGL. It is available for Linux/Unix, Windows and macOS. With Stellarium, you really see what you can see with your eyes, binoculars or a small telescope.
GenomicSQLite - Genomics Extension for SQLite