C++ Bioinformatics

Open-source C++ projects categorized as Bioinformatics

Top 21 C++ Bioinformatic Projects

Bioinformatics
  1. fastp

    An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  2. Stream

    Stream - Scalable APIs for Chat, Feeds, Moderation, & Video. Stream helps developers build engaging apps that scale to millions with performant and flexible Chat, Feeds, Moderation, and Video APIs and SDKs powered by a global edge network and enterprise-grade infrastructure.

    Stream logo
  3. salmon

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment (by COMBINE-lab)

  4. bwa-mem2

    The next version of bwa-mem

  5. bowtie2

    A fast and sensitive gapped read aligner

  6. megahit

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

  7. nanopolish

    Signal-level algorithms for MinION data

  8. edlib

    Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

  9. InfluxDB

    InfluxDB – Built for High-Performance Time Series Workloads. InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.

    InfluxDB logo
  10. hap.py

    Haplotype VCF comparison tools

  11. seqan3

    The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

  12. amr

    AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

  13. octopus

    Bayesian haplotype-based mutation calling (by luntergroup)

  14. bowtie

    An ultrafast memory-efficient short read aligner

  15. rnaseqc

    Fast, efficient RNA-Seq metrics for quality control and process optimization

  16. GenomicSQLite

    Genomics Extension for SQLite

  17. Metabuli

    Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

  18. SnakeStrike

    A Low-cost Open-source High-speed Multi-camera Motion Capture System.

  19. TileDB-VCF

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

  20. sshash

    📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.

  21. IntaRNA

    Efficient target prediction incorporating accessibility of interaction sites

  22. pRIblast

    pRIblast is a high efficient, parallel application for extensive lncRNA-RNA interaction analysis

  23. kmer-signatures

    High-performance kmer-signatures

  24. SaaSHub

    SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

    SaaSHub logo
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).

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C++ Bioinformatics related posts

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    1 project | /r/bioinformatics | 22 Nov 2022
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    1 project | /r/bioinformatics | 12 Oct 2022
  • Tools for strand direction detection RNA-Seq

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  • A note from our sponsor - Stream
    getstream.io | 11 Jul 2025
    Stream helps developers build engaging apps that scale to millions with performant and flexible Chat, Feeds, Moderation, and Video APIs and SDKs powered by a global edge network and enterprise-grade infrastructure. Learn more →

Index

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

# Project Stars
1 fastp 2,118
2 salmon 806
3 bwa-mem2 764
4 bowtie2 723
5 megahit 649
6 nanopolish 585
7 edlib 547
8 hap.py 432
9 seqan3 431
10 amr 315
11 octopus 312
12 bowtie 261
13 rnaseqc 168
14 GenomicSQLite 164
15 Metabuli 140
16 SnakeStrike 99
17 TileDB-VCF 95
18 sshash 87
19 IntaRNA 48
20 pRIblast 2
21 kmer-signatures 0

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