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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
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.
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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
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 |
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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 |