hap.py
Haplotype VCF comparison tools (by Illumina)
megahit
Ultra-fast and memory-efficient (meta-)genome assembler (by voutcn)
| hap.py | megahit | |
|---|---|---|
| 2 | 1 | |
| 392 | 558 | |
| 1.0% | - | |
| 0.0 | 0.0 | |
| 5 months ago | 27 days ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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.
hap.py
Posts with mentions or reviews of hap.py.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Help running hap.py
I have been tasked with benchmarking a variant calling pipeline running hap.py as part of my bioinformatics MSc project.
- cream π
megahit
Posts with mentions or reviews of megahit.
We have used some of these posts to build our list of alternatives
and similar projects.
-
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?
When comparing hap.py and megahit you can also consider the following projects:
GenomicSQLite - Genomics Extension for SQLite
bowtie2 - A fast and sensitive gapped read aligner
seq - A high-performance, Pythonic language for bioinformatics
bwa-mem2 - The next version of bwa-mem
truvari - Structural variant toolkit for VCFs
bowtie - An ultrafast memory-efficient short read aligner
gw - Genome browser and variant annotation
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
nanopolish - Signal-level algorithms for MinION data