Waveform Audio File Format is an audio file format standard for storing an audio bitstream on personal computers. The format was developed and published for the first time in 1991 by IBM and Microsoft. It is the main format used on Microsoft Windows systems for uncompressed audio. The usual bitstream encoding is the linear pulse-code modulation (LPCM) format.
Resource Interchange File Format (RIFF) is a generic file container format for storing data in tagged chunks. It is primarily used for audio and video, though it can be used for arbitrary data.
ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. The ZIP file format permits a number of compression algorithms, though DEFLATE is the most common. This format was originally created in 1989 and was first implemented in PKWARE, Inc.'s PKZIP utility, as a replacement for the previous ARC compression format by Thom Henderson. The ZIP format was then quickly supported by many software utilities other than PKZIP. Microsoft has included built-in ZIP support in versions of Microsoft Windows since 1998 via the "Plus! 98" addon for Windows 98. Native support was added as of the year 2000 in Windows ME. Apple has included built-in ZIP support in Mac OS X 10.3 and later. Most free operating systems have built in support for ZIP in similar manners to Windows and macOS.
The BMP file format or bitmap, is a raster graphics image file format used to store bitmap digital images, independently of the display device, especially on Microsoft Windows and OS/2 operating systems.
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 archiver, also known simply as ar, is a Unix utility that maintains groups of files as a single archive file. Today, ar is generally used only to create and update static library files that the link editor or linker uses and for generating .deb packages for the Debian family; it can be used to create archives for any purpose, but has been largely replaced by tar for purposes other than static libraries. An implementation of ar is included as one of the GNU Binutils.
A FourCC is a sequence of four bytes used to uniquely identify data formats. It originated from the OSType or ResType metadata system used in classic Mac OS and was adopted for the Amiga/Electronic Arts Interchange File Format and derivatives. The idea was later reused to identify compressed data types in QuickTime and DirectShow.
The shapefile format is a geospatial vector data format for geographic information system (GIS) software. It is developed and regulated by Esri as a mostly open specification for data interoperability among Esri and other GIS software products. The shapefile format can spatially describe vector features: points, lines, and polygons, representing, for example, water wells, rivers, and lakes. Each item usually has attributes that describe it, such as name or temperature.
Real-Time Messaging Protocol (RTMP) is a communication protocol for streaming audio, video, and data over the Internet. Originally developed as a proprietary protocol by Macromedia for streaming between Flash Player and the Flash Communication Server, Adobe has released an incomplete version of the specification of the protocol for public use.
In bioinformatics, the general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences.
Action Message Format (AMF) is a binary format used to serialize object graphs such as ActionScript objects and XML, or send messages between an Adobe Flash client and a remote service, usually a Flash Media Server or third party alternatives. The Actionscript 3 language provides classes for encoding and decoding from the AMF format.
FASTQ format is a text-based format for storing both a biological sequence and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute, and became widely known through its implementation within the SAMtools software suite.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM 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, 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 complex - containing reads, references, alignments, quality information, and user-specified annotations - SAMtools reduces the effort needed to use SAM/BAM files by hiding low-level details.
Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species.
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 Sanger Institute, and throughout the 1000 Genomes Project.
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.
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.
ANNOVAR is a bioinformatics software tool for the interpretation and prioritization of single nucleotide variants (SNVs), insertions, deletions, and copy number variants (CNVs) of a given genome.
The BED format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project and then adopted by other sequencing projects. As a result of this increasingly wide use, this format had already become a de facto standard in bioinformatics before a formal specification was written.
