C++ Bioinformatics

Open-source C++ projects categorized as Bioinformatics

Top 21 C++ Bioinformatic Projects

  • fastp

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

  • Project mention: R pipelines for bulk RNA-seq analyses | /r/bioinformatics | 2023-12-09

    fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.

  • salmon

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

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

    InfluxDB logo
  • bwa-mem2

    The next version of bwa-mem

  • bowtie2

    A fast and sensitive gapped read aligner

  • Project mention: NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing | /r/genetics | 2023-09-14

    2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).

  • megahit

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

  • nanopolish

    Signal-level algorithms for MinION data

  • edlib

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

  • WorkOS

    The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

    WorkOS logo
  • hap.py

    Haplotype VCF comparison tools

  • seqan3

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

  • octopus

    Bayesian haplotype-based mutation calling (by luntergroup)

  • bowtie

    An ultrafast memory-efficient short read aligner

  • amr

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

  • GenomicSQLite

    Genomics Extension for SQLite

  • rnaseqc

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

  • SnakeStrike

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

  • TileDB-VCF

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

  • sshash

    A compressed, associative, exact, and weighted dictionary for k-mers.

  • Metabuli

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

  • Project mention: Genomic sequence classification based on k-mers distribution | /r/bioinformatics | 2023-12-04
  • IntaRNA

    Efficient target prediction incorporating accessibility of interaction sites

  • pRIblast

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

  • kmer-signatures

    High-performance kmer-signatures

  • SaaSHub

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

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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).

C++ Bioinformatics related posts


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

Project Stars
1 fastp 1,760
2 salmon 727
3 bwa-mem2 674
4 bowtie2 618
5 megahit 555
6 nanopolish 541
7 edlib 484
8 hap.py 390
9 seqan3 386
10 octopus 296
11 bowtie 252
12 amr 233
13 GenomicSQLite 152
14 rnaseqc 140
15 SnakeStrike 86
16 TileDB-VCF 79
17 sshash 78
18 Metabuli 62
19 IntaRNA 44
20 pRIblast 2
21 kmer-signatures 0

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