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CRAM (file Format)
Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz ''et al''. CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file formats. It optionally uses a genomic reference to describe differences between the aligned sequence fragments and the reference sequence, reducing storage costs. Additionally each column in the SAM format is separated into its own blocks, improving compression ratio. CRAM files typically vary from 30 to 60% smaller than BAM, depending on the data held within them. Implementations of CRAM exist in htsjdk, htslib, JBrowse, and Scramble. The file format specification is maintained by the Global Alliance for Genomics and Health (GA4GH) with the specification document available from the EBI cram toolkit page. File format The basic stru ... [...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 (10s 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 somewhat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally developed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Sequence Format
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments. Biologists are able to study life at multiple levels of organization, from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations.Based on definition from: Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Like other scientists, biologists use the scientific metho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of File Formats
This is a list of file formats used by computers, organized by type. Filename extension it is usually noted in parentheses if they differ from the file format name or abbreviation. Many operating systems do not limit filenames to one extension shorter than 4 characters, as was common with some operating systems that supported the File Allocation Table (FAT) file system. Examples of operating systems that do not impose this limit include Unix-like systems, and Microsoft Windows NT, 95- 98, and ME which have no three character limit on extensions for 32-bit or 64-bit applications on file systems other than pre-Windows 95 and Windows NT 3.5 versions of the FAT file system. Some filenames are given extensions longer than three characters. While MS-DOS and NT always treat the suffix after the last period in a file's name as its extension, in UNIX-like systems, the final period does not necessarily mean that the text after the last period is the file's extension. Some file formats ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Asymmetric Numeral Systems
Asymmetric numeral systems (ANS)J. Duda, K. Tahboub, N. J. Gadil, E. J. Delp''The use of asymmetric numeral systems as an accurate replacement for Huffman coding'' Picture Coding Symposium, 2015.J. Duda''Asymmetric numeral systems: entropy coding combining speed of Huffman coding with compression rate of arithmetic coding'' arXiv:1311.2540, 2013. is a family of entropy encoding methods introduced by Jarosław (Jarek) Duda from Jagiellonian University, used in data compression since 2014 due to improved performance compared to previous methods. ANS combines the compression ratio of arithmetic coding (which uses a nearly accurate probability distribution), with a processing cost similar to that of Huffman coding. In the tabled ANS (tANS) variant, this is achieved by constructing a finite-state machine to operate on a large alphabet without using multiplication. Among others, ANS is used in the Facebook Zstandard compressor [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lempel–Ziv–Markov Chain Algorithm
The Lempel–Ziv–Markov chain algorithm (LZMA) is an algorithm used to perform lossless data compression Lossless compression is a class of data compression that allows the original data to be perfectly reconstructed from the compressed data with no loss of information. Lossless compression is possible because most real-world data exhibits statistic .... It has been under development since either 1996 or 1998 by Igor Pavlov (programmer), Igor Pavlov and was first used in the 7z format of the 7-Zip archiver. This algorithm uses a Dictionary coder, dictionary compression scheme somewhat similar to the LZ77 algorithm published by Abraham Lempel and Jacob Ziv in 1977 and features a high compression ratio (generally higher than bzip2) - LZMA Unix Port was finally replaced by xz which features better and faster compression; from here we know even LZMA Unix Port was a lot better than gzip and bzip2. and a variable compression-dictionary size (up to 4 Gigabyte, GB), while still ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wellcome Sanger Institute
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is located on the Wellcome Genome Campus by the village of Hinxton, outside Cambridge. It shares this location with the European Bioinformatics Institute. It was established in 1992 and named after double Nobel Laureate Frederick Sanger. It was conceived as a large scale DNA sequencing centre to participate in the Human Genome Project, and went on to make the largest single contribution to the gold standard sequence of the human genome. From its inception the institute established and has maintained a policy of data sharing, and does much of its research in collaboration. Since 2000, the institute expanded its mission to understand "the role of genetics in health and disease". The institute now employs around 900 people and engages in five main areas of research: Canc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C (programming Language)
C (''pronounced like the letter c'') is a General-purpose language, general-purpose computer programming language. It was created in the 1970s by Dennis Ritchie, and remains very widely used and influential. By design, C's features cleanly reflect the capabilities of the targeted CPUs. It has found lasting use in operating systems, device drivers, protocol stacks, though decreasingly for application software. C is commonly used on computer architectures that range from the largest supercomputers to the smallest microcontrollers and embedded systems. A successor to the programming language B (programming language), B, C was originally developed at Bell Labs by Ritchie between 1972 and 1973 to construct utilities running on Unix. It was applied to re-implementing the kernel of the Unix operating system. During the 1980s, C gradually gained popularity. It has become one of the measuring programming language popularity, most widely used programming languages, with C compilers avail ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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