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Tabix
Tabix is a free software utility for indexing TAB-delimited genome position files. It is commonly used in bioinformatics analysis to index large genomic data files such as GFF, VCF, or BED files for efficient data retrieval. Tabix was developed by Heng Li and is distributed under the MIT license. Use Tabix requires the input file to be position-sorted and compressed using BGZF. After indexing, Tabix is able to retrieve data lines overlapping query ''intervals'' ''regions'' specified in the format "''chr:start-end''." The index files have a .tbi or .csi extension. It also supports data retrieval over network using direct URL if the index is present in the same location or locally. It also supports multithreading for operations except listing of sequence names. See also * SAMtools SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Software
Free software, libre software, libreware sometimes known as freedom-respecting software is computer software distributed open-source license, under terms that allow users to run the software for any purpose as well as to study, change, distribute it and any adapted versions. Free software is a matter of liberty, not price; all users are legally free to do what they want with their copies of a free software (including profiting from them) regardless of how much is paid to obtain the program.Selling Free Software (GNU) Computer programs are deemed "free" if they give end-users (not just the developer) ultimate control over the software and, subsequently, over their devices. The right to study and modify a computer program entails that the source code—the preferred ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCSC Genome Browser
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website. History Origins and Early Development (2000–2003) The UCSC Genome Browser was developed in 2000 by graduate student Jim Kent and Professor David Haussler at the University of California, Santa Cruz (UCSC), to provide public access to the draft human genome sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of California, Santa Cruz
The University of California, Santa Cruz (UC Santa Cruz or UCSC) is a public university, public Land-grant university, land-grant research university in Santa Cruz, California, United States. It is one of the ten campuses in the University of California system. Located in Monterey Bay, on the edge of the coastal community of Santa Cruz, the main campus lies on of rolling, forested hills overlooking the Pacific Ocean. As of Fall 2024, its ten residential colleges enroll some 17,940 undergraduate and 1,998 graduate students. Satellite facilities in other Santa Cruz locations include the Coastal Science Campus and the Westside Research Park and the Silicon Valley Center in Santa Clara, California, Santa Clara, along with administrative control of the Lick Observatory near San Jose, California, San Jose in the Diablo Range and the W. M. Keck Observatory, Keck Observatory near the summit of Mauna Kea in Hawaii. Founded in 1965, UC Santa Cruz uses a residential college system consist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
O'Reilly Media
O'Reilly Media, Inc. (formerly O'Reilly & Associates) is an American learning company established by Tim O'Reilly that provides technical and professional skills development courses via an online learning platform. O'Reilly also publishes books about programming and other technical content. Its distinctive brand features a woodcut of an animal on many of its book covers. The company was known as a popular tech conference organizer for more than 20 years before closing the live conferences arm of its business. Company Early days The company began in 1978 as a private consulting firm doing technical writing, based in the Cambridge, Massachusetts area. In 1984, it began to retain publishing rights on manuals created for Unix vendors. A few 70-page "Nutshell Handbooks" were well-received, but the focus remained on the consulting business until 1988. After a conference displaying O'Reilly's preliminary Xlib manuals attracted significant attention, the company began increas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heng Li
Heng Li is a Chinese people, Chinese bioinformatics scientist. He is an associate professor at the department of Biomedical Informatics of Harvard Medical School and the department of Data Science of Dana–Farber Cancer Institute, Dana-Farber Cancer Institute. He was previously a research scientist working at the Broad Institute in Cambridge, Massachusetts with David Reich (geneticist), David Reich and David Altshuler (physician), David Altshuler. Li's work has made several important contributions in the field of next generation sequencing. Education Li majored in physics at Nanjing University from 1997 to 2001. He received his PhD from the Institute of Theoretical Physics at the Chinese Academy of Sciences in 2006. His thesis, titled "Constructing the TreeFam database", was supervised by Wei-Mou Zheng. Research Li was involved in a number of projects while working at the Beijing Genomics Institute from 2002 to 2006. These included studying rice finishing, silkworm sequencing, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIT License
The MIT License is a permissive software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts very few restrictions on reuse and therefore has high license compatibility. Unlike copyleft software licenses, the MIT License also permits reuse within proprietary software, provided that all copies of the software or its substantial portions include a copy of the terms of the MIT License and also a copyright notice. In 2015, the MIT License was the most popular software license on GitHub, and was still the most popular in 2025. Notable projects that use the MIT License include the X Window System, Ruby on Rails, Node.js, Lua (programming language), Lua, jQuery, .NET, Angular (web framework), Angular, and React (JavaScript library), React. License terms The MIT License has the identifier MIT in the SPDX License List. It is also known as the "#Ambiguity and variants, Expat License". It has the following terms: Co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug tracking system, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, GitHub, Inc. has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. GitHub reported having over 100 million developers and more than 420 million Repository (version control), repositories, including at least 28 million public repositories. It is the world's largest source code host Over five billion developer contributions were made to more than 500 million open source projects in 2024. About Founding The development of the GitHub platform began on October 19, 2005. The site was launched in April 2008 by Tom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAMtools
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion. SAM files can be very large (tens of Gigabytes is common), so compression is used to save space. SAM files are human-readable text files, and BAM files are simply their binary equivalent, whilst CRAM files are a restructured column-oriented binary container format. BAM files are typically compressed and more efficient for software to work with than SAM. SAMtools makes it possible to work directly with a compressed BAM file, without having to uncompress the whole file. Additionally, since the format for a SAM/BAM file is somewha ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
