C Bioinformatics

Open-source C projects categorized as Bioinformatics
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Topics: Genomics sequence-alignment sequence-analysis Samtools protein-structure
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Top 17 C Bioinformatic Projects

  • minimap2

    A versatile pairwise aligner for genomic and spliced nucleotide sequences

    • Project mention: Ask HN: Comment here about whatever you're passionate about at the moment | news.ycombinator.com | 2023-11-06

    Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.

  • bwa

    Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

    • Project mention: my friend showed me his code, thees are all functions | /r/ProgrammerHumor | 2023-05-25

    Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h

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  • seqtk

    Toolkit for processing sequences in FASTA/Q formats

    • Project mention: Illumina adapters and quality trimming | /r/bioinformatics | 2023-07-04

    seqtk: A lightweight and versatile tool for processing FASTQ and FASTA files. https://github.com/lh3/seqtk

  • MMseqs2

    MMseqs2: ultra fast and sensitive search and clustering suite

  • htslib

    C library for high-throughput sequencing data formats

    • Project mention: Gentoo -Os vs -O3 application startup time? | /r/Gentoo | 2023-06-29

  • foldseek

    Foldseek enables fast and sensitive comparisons of large structure sets.

  • bioawk

    BWK awk modified for biological data

    • Project mention: Bioawk: Awk Modified for Biological Data | news.ycombinator.com | 2024-03-31

  • 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.

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  • hh-suite

    Remote protein homology detection suite.

  • miniprot

    Align proteins to genomes with splicing and frameshift

  • kent

    UCSC Genome Browser source tree. Stable branch: "beta".

  • biowasm

    WebAssembly modules for genomics

    • Project mention: Biowasm – Run C/C++ genomics tools in the browser | news.ycombinator.com | 2024-03-11

  • biofast

    Benchmarking programming languages/implementations for common tasks in Bioinformatics

  • readfq

    Fast multi-line FASTA/Q reader in several programming languages

  • MethylDackel

    A (mostly) universal methylation extractor for BS-seq experiments.

  • libBigWig

    A C library for handling bigWig files

  • libdna

    ♥ Essential Functions for DNA Manipulation

  • bam-filter

    Use simple expressions to filter a BAM/CRAM file

  • SaaSHub

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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

Index

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

Project Stars
1 minimap2 1,679
2 bwa 1,443
3 seqtk 1,308
4 MMseqs2 1,246
5 htslib 771
6 foldseek 632
7 bioawk 572
8 hh-suite 498
9 miniprot 296
10 kent 204
11 biowasm 186
12 biofast 175
13 readfq 164
14 MethylDackel 151
15 libBigWig 70
16 libdna 20
17 bam-filter 5

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