C Genomics

Open-source C projects categorized as Genomics
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Bioinformatics bam sequence-alignment Crystal Compression
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Top 5 C Genomic Projects

Genomics

  1. minimap2

    A versatile pairwise aligner for genomic and spliced nucleotide sequences

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  3. bwa

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

  4. cgranges

    A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

    Project mention: Ask HN: Fast data structures for disjoint intervals? | news.ycombinator.com | 2024-07-23

    You're looking for an implicit interval tree. The key idea is to store sorted ranges and simulate the interval tree via binary search. The best implementation I know of is coitrees: https://github.com/dcjones/coitrees, but you could also roll your own. cgranges is another good implementation: https://github.com/lh3/cgranges

  5. genozip

    A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

  6. bam-filter

    Use simple expressions to filter a BAM/CRAM file

  7. InfluxDB

    InfluxDB high-performance time series database. Collect, organize, and act on massive volumes of high-resolution data to power real-time intelligent systems.

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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 Genomics discussion

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C Genomics related posts

  • Biowasm – Run C/C++ genomics tools in the browser

    1 project | news.ycombinator.com | 11 Mar 2024

  • BLAST 10,000 genes?

    1 project | /r/bioinformatics | 25 Feb 2023

  • Truncating genome fastas to just overlapping regions

    1 project | /r/bioinformatics | 19 Jan 2023

  • We're wasting money by only supporting gzip for raw DNA files

    6 projects | news.ycombinator.com | 9 Jan 2023

  • Alignment of long reads to plasmid and generation of consensus sequence.

    1 project | /r/bioinformatics | 26 Oct 2022

  • Scientists Are Finding Fungi in Cancerous Tumors

    3 projects | news.ycombinator.com | 10 Oct 2022

  • Show HN: I built interactive playgrounds for Awk, sed, grep using WebAssembly

    1 project | news.ycombinator.com | 21 Jul 2022
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Index

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

# Project Stars
1 minimap2 1,931
2 bwa 1,597
3 cgranges 168
4 genozip 165
5 bam-filter 5

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