C++ Genomics

Open-source C++ projects categorized as Genomics

Top 11 C++ Genomic Projects

  • vg

    tools for working with genome variation graphs (by vgteam)

  • seq

    A high-performance, Pythonic language for bioinformatics

  • Sonar

    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

    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

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

  • bowtie2

    A fast and sensitive gapped read aligner

  • megahit

    Ultra-fast and memory-efficient (meta-)genome assembler

  • hap.py

    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

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

  • octopus

    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

    An ultrafast memory-efficient short read aligner

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

    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

    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.

C++ Genomics related posts

Index

What are some of the best open-source Genomic projects in C++? This list will help you:

Project Stars
1 vg 865
2 seq 622
3 bwa-mem2 574
4 Vcflib 522
5 bowtie2 484
6 megahit 431
7 hap.py 330
8 octopus 268
9 bowtie 238
10 GenomicSQLite 132
11 TileDB-VCF 54
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