sgkit
We've moved to https://github.com/sgkit-dev/sgkit (by pystatgen)
TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
| sgkit | TileDB-VCF | |
|---|---|---|
| 1 | 4 | |
| 0 | 80 | |
| - | - | |
| 5.9 | 8.6 | |
| about 2 months ago | about 5 hours ago | |
| HTML | C++ | |
| Apache License 2.0 | 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.
sgkit
Posts with mentions or reviews of sgkit.
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?
I once built on top of a library that used the zarr format for storing the vcf data. It allowed me to parse over it like it was a pandas dataframe and incredibly fast. sgkit is the successor library and seems to be growing really well, but I haven't played with it. I do have high hopes for the zarr format, but I am biased
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.
-
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
What are some alternatives?
When comparing sgkit and TileDB-VCF you can also consider the following projects:
Dask - Parallel computing with task scheduling
Hail - Cloud-native genomic dataframes and batch computing
gwas2vcf - Convert GWAS summary statistics to VCF
truvari - Structural variant toolkit for VCFs
Scoary - Pan-genome wide association studies
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
TileDB - The Universal Storage Engine
gw - Genome browser and variant annotation
octopus - Bayesian haplotype-based mutation calling
hap.py - Haplotype VCF comparison tools