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Top 21 C++ Bioinformatic Projects
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fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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Stream
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salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment (by COMBINE-lab)
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edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
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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.
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seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
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amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
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Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
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TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
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pRIblast
pRIblast is a high efficient, parallel application for extensive lncRNA-RNA interaction analysis
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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 discussion
C++ Bioinformatics related posts
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Ask HN: Comment here about whatever you're passionate about at the moment
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NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
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Illumina's Manta candidateSmallIndels.vcf.gz Fed Into Illumina's Strelka Using What Sample's candidateSmallIndels.vcf.gz Experimental/Tumor or Normal?
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What to do with Manta outputs
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Help running hap.py
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Anyone use DRAGEN-GATK?
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Tools for strand direction detection RNA-Seq
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A note from our sponsor - Stream
getstream.io | 11 Jul 2025
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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