Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts
☆11Dec 11, 2020Updated 5 years ago
Alternatives and similar repositories for htslib_howto
Users that are interested in htslib_howto are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- Day 2 of ACAD's 2018 Advanced Bioinformatics Workshop☆12Nov 27, 2018Updated 7 years ago
- A efficient method to construct BWT index of a given DNA sequence, especially useful for gigantic and high similar genome.☆15May 4, 2016Updated 9 years ago
- Five implementations of double linked lists to demonstrate generic data structures in C☆18Dec 19, 2019Updated 6 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 3 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Aug 8, 2018Updated 7 years ago
- Read CRAM v3 and v2 in node or in the browser☆18Updated this week
- Build an index for your BAM Index (BAI)☆17Apr 14, 2015Updated 10 years ago
- A simple example of parsing BAM files using htslib☆12Mar 22, 2016Updated 10 years ago
- deSAMBA: fast and accurate classification of metagenomics long reads with sparse approximate matches☆12May 5, 2024Updated last year
- ☆15Mar 9, 2018Updated 8 years ago
- ☆20Aug 18, 2020Updated 5 years ago
- Tutorial on programming or "big data"/bioinformatics☆32Jan 5, 2018Updated 8 years ago
- Numerical Encoding for Human Genetic Variants☆42Jun 8, 2023Updated 2 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Linear-time, low-memory construction of variation graphs☆20Feb 3, 2020Updated 6 years ago
- Recommendations to contenarized your bioinformatics software☆12May 30, 2018Updated 7 years ago
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Jan 28, 2026Updated last month
- Ultra-fast, high-performing structural variation (SV) detector☆24Apr 26, 2023Updated 2 years ago
- Quickly calculate and visualize sequence coverage in alignment files☆100Jun 22, 2019Updated 6 years ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- IndexTools is a toolkit for extremely fast NGS analysis based on index files.☆17Aug 19, 2022Updated 3 years ago
- Variant Call Format (VCF) parser☆26Feb 28, 2026Updated 3 weeks ago
- Static Huffman coding☆10Apr 3, 2017Updated 8 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆21Dec 26, 2025Updated 2 months ago
- A Strategy for Building and Using a Human Reference Pangenome☆70May 29, 2020Updated 5 years ago
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆138Sep 16, 2025Updated 6 months ago
- ☆27Oct 11, 2025Updated 5 months ago
- Streaming assembly for MinION data☆25Dec 16, 2023Updated 2 years ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 9 months ago
- A long-read analysis toolbox for cancer and population genomics☆23Jul 1, 2025Updated 8 months ago
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Jul 19, 2024Updated last year
- C implementation of the Landau-Vishkin algorithm☆35Apr 8, 2022Updated 3 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Alignment-free detection of structural variations and viral integrations in circulating tumor DNA☆17Nov 11, 2021Updated 4 years ago
- Python library to handle different kind of operations with the OANDA API☆11Dec 23, 2024Updated last year
- ☆11Aug 5, 2021Updated 4 years ago
- toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files☆22Aug 13, 2024Updated last year
- a GFA toolkit☆13Oct 4, 2024Updated last year
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- R package specialized in HLA typing clustering and visualization based on specific similarity metrics☆14Nov 21, 2019Updated 6 years ago