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MPEG-G
MPEG-GISO / IEC 23092 is an ISO/IEC standard designed for genomic information representation by the collaboration of the ISO/IEC JTC 1/SC 29/WG 9 (MPEG) anISO TC 276 "Biotechnology"Work Group 5. The goal of the standard is to provide interoperable solutions for data storage, access, and protection across different possible implementations for data information generated by high-throughput sequencing machines and their subsequent processing and analysis. The standard is composed of different parts, each one addressing a specific aspect, such as compression, metadata association, Application Programming Interfaces (APIs), and a reference software for data decoding. Together with the reference decoder software, commercial and open source implementations started to be available in 2019, covering progressively more of the published parts of the standard. Background The advent of high-throughput sequencing (HTS) technologies has revolutionized the field of quantitative biology. Availabi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MPEG-G
MPEG-GISO / IEC 23092 is an ISO/IEC standard designed for genomic information representation by the collaboration of the ISO/IEC JTC 1/SC 29/WG 9 (MPEG) anISO TC 276 "Biotechnology"Work Group 5. The goal of the standard is to provide interoperable solutions for data storage, access, and protection across different possible implementations for data information generated by high-throughput sequencing machines and their subsequent processing and analysis. The standard is composed of different parts, each one addressing a specific aspect, such as compression, metadata association, Application Programming Interfaces (APIs), and a reference software for data decoding. Together with the reference decoder software, commercial and open source implementations started to be available in 2019, covering progressively more of the published parts of the standard. Background The advent of high-throughput sequencing (HTS) technologies has revolutionized the field of quantitative biology. Availabi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MPEG
The Moving Picture Experts Group (MPEG) is an alliance of working groups established jointly by International Organization for Standardization, ISO and International Electrotechnical Commission, IEC that sets standards for media coding, including compression coding of audio compression (data), audio, video compression, video, graphics, and Compression of Genomic Sequencing Data, genomic data; and transmission and Container format (digital), file formats for various applications.John Watkinson, ''The MPEG Handbook'', p. 1 Together with Joint Photographic Experts Group, JPEG, MPEG is organized under ISO/IEC JTC 1/ISO/IEC JTC 1/SC 29, SC 29 – ''Coding of audio, picture, multimedia and hypermedia information'' (ISO/IEC Joint Technical Committee 1, Subcommittee 29). MPEG formats are used in various multimedia systems. The most well known older MPEG media formats typically use MPEG-1, MPEG-2, and MPEG-4 AVC media coding and MPEG-2 systems MPEG transport stream, transport streams an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
ISO/IEC
ISO/IEC JTC 1, entitled "Information technology", is a joint technical committee (JTC) of the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC). Its purpose is to develop, maintain and promote standards in the fields of information and communications technology (ICT). JTC 1 has been responsible for many critical IT standards, ranging from the Joint Photographic Experts Group (JPEG) image formats and Moving Picture Experts Group (MPEG) audio and video formats to the C and C++ programming languages. History ISO/IEC JTC 1 was formed in 1987 as a merger between ISO/TC 97 (Information Technology) and IEC/TC 83, with IEC/SC 47B joining later. The intent was to bring together, in a single committee, the IT standardization activities of the two parent organizations in order to avoid duplicative or possibly incompatible standards. At the time of its formation, the mandate of JTC 1 was to develop base standards in information tec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ISO/IEC JTC 1/SC 29
ISO/IEC JTC 1/SC 29, entitled ''Coding of audio, picture, multimedia and hypermedia information'', is a standardization subcommittee of the Joint Technical Committee ISO/IEC JTC 1 of the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC). It develops and facilitates international standards, technical reports, and technical specifications within the field of audio, picture, multimedia, and hypermedia information coding. The standards developed by SC 29 have been recognized by nine Emmy Awards. The international secretariat of SC 29 is the Japanese Industrial Standards Committee (JISC) of Japan. History ISO/IEC JTC 1/SC 29 was established in 1991, when the subcommittee took over the tasks of ISO/IEC JTC 1/SC 2/WG 8. Its title, "Coded representation of audio, picture, multimedia and hypermedia information", has not been changed since its inception. Within its first year, SC 29 established four working groups, a secretariat, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High-throughput Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid speed of sequencing attained with modern DNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, it has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. As of June 2022, GitHub reported having over 83 million developers and more than 200 million repositories, including at least 28 million public repositories. It is the largest source code host . History GitHub.com Development of the GitHub.com platform began on October 19, 2007. The site was launched in April 2008 by Tom Preston-Werner, Chris Wanstrath, P. J. Hyett and Scott Chacon after it had been made available for a few months prior as a beta release. GitHub has an annual keynote called GitHub Universe. Organizational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like the R programming language, Python, Ruby, Haskell, and Perl. Original format & overview The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number). In the original format, a sequence was represented as a series of lines, each of whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTQ Format
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA formatted sequence and its quality data, but has recently become the ''de facto'' standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer. Format A FASTQ file has four line-separated fields per sequence: * Field 1 begins with a '@' character and is followed by a sequence identifier and an ''optional'' description (like a FASTA title line). * Field 2 is the raw sequence letters. * Field 3 begins with a '+' character and is ''optionally'' followed by the same sequence identifier (and any description) again. * Field 4 encodes the quality values for the sequence in Field 2, and must contain the same num ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAM (file Format)
Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker ''et al''. It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format. The overall TAB-delimited flavour of the format came from an earlier format inspired by BLAT’s PSL. The name of SAM came from Gabor Marth from University of Utah, who originally had a format under the same name but with a different syntax more similar to a BLAST output. It is widely used for storing data, such as nucleotide sequences, generated by next generation sequencing technologies, and the standard has been broadened to include unmapped sequences. The format supports short and long reads (up to 128 Mbp) produced by different sequencing platforms and is used to hold mapped data within the Genome Analysis Toolkit (GATK) and across the Broad Institute, the Wellcome S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binary Alignment Map
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format. The structure of BAM files include a header section and an alignment section: * Header—The sample name, sample length, and alignment method are all included in this section. The alignments section contains alignments that are linked to specific information in the header section. * Alignments—The read name, read sequence, read quality, alignment information, and custom tags are all included in this file. The chr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ISO/IEC Standards
ISO/IEC JTC 1, entitled "Information technology", is a joint technical committee (JTC) of the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC). Its purpose is to develop, maintain and promote standards in the fields of information and communications technology (ICT). JTC 1 has been responsible for many critical IT standards, ranging from the Joint Photographic Experts Group (JPEG) image formats and Moving Picture Experts Group (MPEG) audio and video formats to the C and C++ programming languages. History ISO/IEC JTC 1 was formed in 1987 as a merger between ISO/TC 97 (Information Technology) and IEC/TC 83, with IEC/SC 47B joining later. The intent was to bring together, in a single committee, the IT standardization activities of the two parent organizations in order to avoid duplicative or possibly incompatible standards. At the time of its formation, the mandate of JTC 1 was to develop base standards in information tec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
