megahit
Ultra-fast and memory-efficient (meta-)genome assembler (by voutcn)
bwa-mem2
The next version of bwa-mem (by bwa-mem2)
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| megahit | bwa-mem2 | |
|---|---|---|
| 1 | 2 | |
| 554 | 674 | |
| - | 1.5% | |
| 0.0 | 2.6 | |
| 15 days ago | 4 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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
Posts with mentions or reviews of megahit.
We have used some of these posts to build our list of alternatives
and similar projects.
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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.
bwa-mem2
Posts with mentions or reviews of bwa-mem2.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-06-28.
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Anyone use DRAGEN-GATK?
If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
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Software Development Project
I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true). https://github.com/bwa-mem2/bwa-mem2
What are some alternatives?
When comparing megahit and bwa-mem2 you can also consider the following projects:
bowtie2 - A fast and sensitive gapped read aligner
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
hap.py - Haplotype VCF comparison tools
seq - A high-performance, Pythonic language for bioinformatics
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
bowtie - An ultrafast memory-efficient short read aligner
htslib - C library for high-throughput sequencing data formats
nanopolish - Signal-level algorithms for MinION data
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
octopus - Bayesian haplotype-based mutation calling
seqstats - Quick summary statistics on fasta/fastq(.gz) files