TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
gwas2vcf
Convert GWAS summary statistics to VCF (by MRCIEU)
| TileDB-VCF | gwas2vcf | |
|---|---|---|
| 4 | 1 | |
| 80 | 39 | |
| - | - | |
| 8.6 | 0.0 | |
| 3 days ago | about 1 year ago | |
| C++ | Python | |
| MIT License | MIT License |
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.
TileDB-VCF
Posts with mentions or reviews of TileDB-VCF.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-11-12.
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Has anyone stored/queried VCFs and their variant records in a relational database?
Perhaps of interest https://github.com/TileDB-Inc/TileDB-VCF
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[TileDB webinar] Population genomics is a data management problem
Here are the docs to the open-source TileDB-VCF storage engine: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics
gwas2vcf
Posts with mentions or reviews of gwas2vcf.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-09-01.
-
Nuitka: An extremely compatible Python compiler
Here is the original repo I have tried to speed up using:
python -m nuitka --clang --follow-imports main.py
repo: https://github.com/MRCIEU/gwas2vcf
If someone can make the program run faster by whatever means, it will make a bunch of people quite happy.
What are some alternatives?
When comparing TileDB-VCF and gwas2vcf you can also consider the following projects:
Hail - Cloud-native genomic dataframes and batch computing
truvari - Structural variant toolkit for VCFs
graalvm-ten-things - Top 10 Things To Do With GraalVM
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
pybenchmarks - Python Interpreters Benchmarks
TileDB - The Universal Storage Engine
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
gw - Genome browser and variant annotation
py2many - Transpiler of Python to many other languages