hap.py
Haplotype VCF comparison tools (by Illumina)
GenomicSQLite
Genomics Extension for SQLite (by mlin)
Our great sponsors
| hap.py | GenomicSQLite | |
|---|---|---|
| 2 | 1 | |
| 390 | 152 | |
| 2.1% | - | |
| 0.0 | 3.4 | |
| 4 months ago | 3 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
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
GenomicSQLite
Posts with mentions or reviews of GenomicSQLite.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-07-31.
-
sqlite-zstd: Transparent dictionary-based row-level compression for SQLite - An SQLite extension written in Rust to reduce the database size without losing functionality
Yes, that is indeed an obviously missing part. I knew about ZIPVFS, but somehow forgot to investigate closer. Probably because I started this project before GenomicsSQLite was a thing (that seems like the best alternative).
What are some alternatives?
When comparing hap.py and GenomicSQLite you can also consider the following projects:
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
FlatBuffers - FlatBuffers: Memory Efficient Serialization Library
gw - Genome browser and variant annotation
bwa-mem2 - The next version of bwa-mem
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
truvari - Structural variant toolkit for VCFs
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.