Top 11 C++ Genomic Projects

vg

0 865 9.8 C++

tools for working with genome variation graphs (by vgteam)
seq

0 622 0.6 C++

A high-performance, Pythonic language for bioinformatics
Sonar

sonarsource.zoom.us
sponsored

Free webinar: The Power of Clean C++. Are you ready to take your C++ code to the next level? Join Sonar on December 7th for our live webinar as we discuss how to get your code clean - and stay clean - with minimal effort and without being overloaded with warnings. Register now!
bwa-mem2

2 574 0.6 C++

The next version of bwa-mem

Project mention: Anyone use DRAGEN-GATK? | reddit.com/r/bioinformatics | 2022-10-12

If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
Vcflib

0 522 9.4 C++

C++ library and cmdline tools for parsing and manipulating VCF files
bowtie2

0 484 8.7 C++

A fast and sensitive gapped read aligner
megahit

0 431 0.0 C++

Ultra-fast and memory-efficient (meta-)genome assembler
hap.py

2 330 0.6 C++

Haplotype VCF comparison tools

Project mention: Help running hap.py | reddit.com/r/bioinformatics | 2022-11-22

I have been tasked with benchmarking a variant calling pipeline running hap.py as part of my bioinformatics MSc project.
Zigi

www.zigi.ai
sponsored

Workflow assistant built for devs & their teams. Automate the mundane part of your day, with live actionable messages for your GitHub & Jira tasks.
octopus

1 268 8.6 C++

Bayesian haplotype-based mutation calling (by luntergroup)

Project mention: genotyping tool | reddit.com/r/bioinformatics | 2022-07-13

Check out octopus https://github.com/luntergroup/octopus
bowtie

1 238 10.0 C++

An ultrafast memory-efficient short read aligner

Project mention: Burrows–Wheeler Transform | news.ycombinator.com | 2022-09-24
GenomicSQLite

1 132 4.9 C++

Genomics Extension for SQLite

Project mention: sqlite-zstd: Transparent dictionary-based row-level compression for SQLite - An SQLite extension written in Rust to reduce the database size without losing functionality | reddit.com/r/rust | 2022-07-31

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).
TileDB-VCF

1 54 7.3 C++

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Project mention: Has anyone stored/queried VCFs and their variant records in a relational database? | reddit.com/r/bioinformatics | 2022-11-12

Perhaps of interest https://github.com/TileDB-Inc/TileDB-VCF

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2022-11-22.