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Samtools
Samtools offers a suite of open-source tools for working with high-throughput sequencing data, helping researchers process and analyze genomic datasets.
Process and analyze sequencing data with ease
Samtools is a collection of open-source programs designed for scientists and researchers who work with high-throughput sequencing data. With this suite, you can easily convert, manipulate, and analyze formats like BAM, CRAM, and VCF, making it a versatile toolkit for genomic data workflows.
Whether you need to convert raw sequencing reads, mark duplicates, filter variant files, or integrate with related tools, Samtools provides robust solutions all in one place. The website offers downloads, documentation, and helpful guides to get you started, so you can focus on your research and data analysis without unnecessary hassle.
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Jalview is a free program for editing, visualizing, and analyzing multiple sequence alignments, offering tools for phylogenetic trees and molecular structures.
Find clear, up-to-date documentation for ANNOVAR, a software tool used to annotate genetic variants across human and other genomes.
BioCyc offers integrated genome and metabolic pathway data for thousands of organisms, plus bioinformatics tools for research and analysis.
PCRE offers a free library for Perl-compatible regular expression pattern matching, with APIs for developers and full documentation for integration.
Download, use, and learn about GMP, an open-source C library for arbitrary-precision arithmetic, with documentation and source code available.
MinGW.org offers tools for setting up a Windows development environment with GCC, making it easy to compile and build native Windows programs.
Apache Xerces offers open-source software libraries for creating and managing XML data in Java, C++, and Perl, supporting developers and organizations.
MiKTeX offers an easy way to install and use TeX for creating documents on Windows, Linux, and macOS, with helpful tools and support resources.
Biopython offers free Python tools for biological computation, making it easier for scientists and developers to analyze biological data and build new tools.
CLever Audio Plug-In (CLAP) is an open standard for audio plug-ins and hosts, offering tools and resources for audio software developers.
PyYAML is a framework for Python that helps you easily read and write YAML files, making it simple to work with configuration and data files.
py2exe lets you turn Python scripts into Windows executables, so your programs run on Windows computers without needing a Python installation.
Choco-solver is an open-source Java library for constraint programming, offering tools and documentation to help developers solve complex problems.
Open MPI provides an open source toolkit for high performance computing, enabling fast message passing and parallel processing on clusters and supercomputers.
SWIG is a free tool that helps connect C and C++ code with many other programming languages, making it easier to build interfaces and prototypes.
Download FFTW, a free C library for fast Fourier transforms, with support for real/complex, multidimensional, and parallel signal processing.
Access ICU source code, tools, and documentation for internationalization support in software development. Site has moved to icu.unicode.org.
Xolstice offers software tools and plugins for developers, including the Maven Protocol Buffers Plugin, with updates and downloads since 2008.
Download official LLVM releases, including compilers and tools for building software projects, all under an open-source license.
Paramiko is a Python library for SSH connections, letting you securely run remote commands and transfer files in your own Python projects.
Rakudo offers downloads, documentation, and community for the Rakudo compiler, helping you use the Raku programming language with ease.
Nokogiri helps Ruby developers easily read, write, and modify XML and HTML with clear guides, tutorials, and detailed documentation.
LLVM offers modular compiler and toolchain technologies for building and customizing programming languages and development tools.
Apache Maven helps you manage software projects, automating builds, reporting, and documentation from a single, central platform.
FreeType is a free, portable software library for rendering fonts, supporting TrueType, OpenType, and more for developers and projects worldwide.
Explore safe Rust bindings for GTK and GNOME libraries, making it easier for developers to build desktop apps using modern Rust and the GNOME stack.
Capstone is a lightweight, multi-platform disassembly framework for developers, offering support for multiple architectures and easy integration.
Knopflerfish OSGi is an open source platform and SDK for building and running OSGi-based modular Java applications, supporting multiple OSGi releases.
OpenVDB is an open-source C++ library for efficient 3D volumetric data storage and manipulation, used in animation, VFX, and digital art projects.
Keystone is an assembler engine based on LLVM, letting you turn assembly code into machine code. Download, explore docs, and integrate it in your projects.
Worldwide Htslib.org Alternatives
Burrows-Wheeler Aligner (BWA) is a software tool for mapping DNA sequences to reference genomes, supporting both short and long read alignment.
Access information and downloads for older versions of SAMtools, a toolkit for working with DNA sequencing data in bioinformatics projects.
Explore open-source tools, libraries, and file format specs for next-generation DNA sequencing developers, including C and Java APIs from Samtools.
Bowtie offers a fast and efficient tool for aligning short DNA sequences to genomes, making it easier for researchers to analyze large-scale genetic data.
MAFFT is an online tool for multiple sequence alignment, helping researchers quickly align DNA or protein sequences for bioinformatics analysis.
Genome Modeling Tools offers resources and downloads for genomic data analysis, including support for TIGRA-SV and related research tools.
Explore detailed documentation for bcbio-nextgen, a Python toolkit offering automated pipelines for high-throughput sequencing analysis in bioinformatics.
TIDE analyzes DNA sequencing data to quickly identify and quantify genome editing mutations, helping researchers assess CRISPR and similar experiments easily.
PRINSEQ helps you quickly clean and check DNA sequence data for bioinformatics and metagenomics research. Simple tools for quality control and preprocessing.
UGENE is a free, open-source bioinformatics toolkit for visualizing, aligning, assembling, and annotating DNA and protein sequences.
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