TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library. (by TileDB-Inc)
hap.py
Haplotype VCF comparison tools (by Illumina)
| TileDB-VCF | hap.py | |
|---|---|---|
| 4 | 2 | |
| 80 | 393 | |
| - | 1.3% | |
| 8.6 | 0.0 | |
| 4 days ago | 5 months ago | |
| C++ | C++ | |
| MIT License | 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.
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
-
[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
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
What are some alternatives?
When comparing TileDB-VCF and hap.py you can also consider the following projects:
Hail - Cloud-native genomic dataframes and batch computing
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
gwas2vcf - Convert GWAS summary statistics to VCF
GenomicSQLite - Genomics Extension for SQLite
truvari - Structural variant toolkit for VCFs
seq - A high-performance, Pythonic language for bioinformatics
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
sgkit - We've moved to https://github.com/sgkit-dev/sgkit