516 Open source projects that are alternatives of or similar to Htslib

A Java API for high-throughput sequencing data (HTS) formats.

Method to optimally select samples for validation and resequencing

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

(No maintenance) Detect gene fusion directly from raw fastq files

UGENE is free open-source cross-platform bioinformatics software

NGLess: NGS with less work

My bioinfo toolbox

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Tools to process and analyze deep sequencing data.

Genotyping of segregating mobile elements insertions

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

highly-efficient & lightweight mutation signature matrix aggregation

Scalable genomic data analysis.

Structural variant toolkit for VCFs

A collection of scripts and notes related to genomics and bioinformatics

Tools for working with genomic and high throughput sequencing data.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A DNA Sequence Alignment/Map (SAM) library for Clojure

Syntax highlighting for computational biology

Simple pure Python SAM parser and objects for working with SAM records

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Project metadata manager for PEPs in Python

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

A simplified pipeline for ctDNA sequencing data analysis

Haplotype VCF comparison tools

A package for designing compact and comprehensive capture probe sets.

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Frequently used commands in bioinformatics

A robust model for quantitative comparison of ChIP-Seq data sets.

Data intensive science for everyone.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Bayesian genotyper for structural variants

Official code repository for GATK versions 4 and up

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Syntax highlighting for computational biology

R package for analyzing single-cell RNA-seq data

Toolset for SV simulation, comparison and filtering

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

annotate a VCF with other VCFs/BEDs/tabixed files

cython + htslib == fast VCF and BCF processing

Tools for working with SAM/BAM data

A D library for computational biology and bioinformatics

Java utilities for Bioinformatics

Interactive network visualization in Python and Dash, powered by Cytoscape.js

The next version of bwa-mem

Bioinformatics one liners from Ming Tang

Efficient pythonic random access to fasta subsequences

MMseqs2: ultra fast and sensitive search and clustering suite

Python library to facilitate genome assembly, annotation, and comparative genomics

A comprehensive tutorial about GWAS and PRS

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

A modern genome browser built with JavaScript and HTML5.

Modular and universal bioinformatics

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics