nanopolish
megahit
| nanopolish | megahit | |
|---|---|---|
| 1 | 1 | |
| 542 | 563 | |
| - | - | |
| 5.2 | 0.0 | |
| 9 months ago | 14 days ago | |
| C++ | C++ | |
| MIT License | GNU General Public License v3.0 only |
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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).
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.
What are some alternatives?
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
bowtie2 - A fast and sensitive gapped read aligner
bowtie - An ultrafast memory-efficient short read aligner
hap.py - Haplotype VCF comparison tools
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
bwa-mem2 - The next version of bwa-mem
opensim-core - SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
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.
seq - A high-performance, Pythonic language for bioinformatics
octopus - Bayesian haplotype-based mutation calling
GenomicSQLite - Genomics Extension for SQLite