| FASTQ |
FASTQ format |
A (text-based) format that is used for storing a biological sequence (typically a nucleotide sequence) and its corresponding quality scores. The sequence letter and quality score are encoded using a single ASCII character. |
| BAM |
binary alignment map format |
A format that is the compressed binary representation of a sequence alignment map format. |
| TIFF |
tag image file format |
A format that is for storing raster graphics images. |
| SWC |
SWC file format, SWC neuron morphology format |
A format that is used to store neuron morphology data, to share information to digitally reconstruct neurons, and to predict functional attributes using simulation environments. |
| NWB |
neurodata without borders format, NWB format, NWB file format |
A format that is designed to store a wide range of neurophysiology data. It is a HDF5 file that has data organized by including a dedicated location for storing all data that is acquired during an experiment as well as another location to store stimulus data that was presented. |
| browser extensible data format |
BED, browser extensible data file format, BED format, BED file format |
A format that is a text file used to store data regarding genomic regions as coordinates and associated annotations. |
| bigBed |
bigBed format, bigBed file format |
A format that is created from a BED file that stores annotation items that are simple or a linked collection of exons. They are in an indexed binary format. |
| comma-separated values format |
CSV, CSV format, CSV file format |
A format that is a delimited text file that uses a comma to separate values. Each line of the file is a data record, and each record consists of one or more fields, separated by commas. |
| MTX |
MTX format, MTX file format |
A format that is associated with a 3D scene format consisting of a ASCII text written using XML-style tags representing 3D object hierarchies, animation data, and global scene options. |
| tab-separated values format |
TSV, TSV format, TSV file format |
A format that is a text file format used to store data in a tabular structure, for example, a database table or spreadsheet data. It is also used as a means of exchanging information between databases. |
| H5 |
HDF5, hierarchical data format 5 |
A format that contains multidimensional arrays of scientific data. |
| Loom |
Loom format |
A format that is designed to hold large -omics datasets. The format is based on HDF5 in that it is an HDF5 file that contains specific groups containing the main matrix as well as row and column attributes. |
| PLINK.bed |
.bed PLINK file |
A format that is a binary text file format for PLINK that serves as input for analysis. This is the preferred file type for representing genotype calls for PLINK. |
| bim |
.bim file, .bim format, PLINK extended MAP file |
A format that is a variant information file accompanying a .bed or biallelic .pgen binary genotype table. |
| fam |
.fam file, .fam format, PLINK sample information file |
A format that is a sample information file accompanying a .bed or biallelic .pgen binary genotype table. |
| brain imaging data structure |
BIDS, BIDS format, BIDS file format, brain imaging data structure file format |
A format that is a standard for organizing and describing neuroimaging and behavioral data. |
| H5AD |
H5AD format |
A HDF5 file format that provides a scalable way of keeping track of data together with learned annotations. It is anndata's native file format. |
| NGFF |
NGFF format, zarr file, Next-generation file format |
A format that is designed to hold information about multidimensional, multiscale images, high-content screening datasets and derived labeled images. They are able to be hosted natively in an object (or cloud) storage for direct access by a large number of users. |
| Nifti file format |
Nifti format, nii file |
A format that is designed for neuroimaging data that is similar to the Analyze for the storage of Functional Magnetic Resonance Imaging (fMRI) and other medical images. |
| JSON |
JSON format, json file, JavaScript Object Notation, JavaScript Object Notation format |
A format that is an open standard file format and data interchange format that uses human-readable text consisting of attribute-value pairs and arrays to store and transmit data. |
| JSON-LD |
JSON-LD format, JSON-LD file, JavaScript Object Notation for Linked Data |
A format that is an open standard file format and data interchange format that uses human-readable text consisting of attribute-value pairs and arrays to store and transmit data in addition to a linked data (LD) element. |
| OME TIFF |
OME-TIFF file, OME-TIFF format |
A format for storing microscopy imaging data created to maximize the respective strengths of OME-XML and TIFF. It takes advantage of metadata defined in OME-XML while retaining the pixels in multi-page TIFF format for compatibility with many more applications. |
| mex |
mex format, mex file |
A format that is used to represent the gene-barcode matrix output by Cell Ranger. This is a sparse matrix format because the matrix for UMI counts for each barcode/gene pair are very large (~35K genes vs hundreds of thousands of barcodes) and most entries are 0. |
| scn |
scn format, scn file |
A format that is used in digital pathology, which is a proprietary format used by Leica Biosystems scanners to store whole slide images (WSIs). |
| docx |
docx format, docx file, Microsoft Word Open XML Document |
A format that is used as the default, modern Microsoft Word document format that uses Office Open XML (OOXML), a zipped archive of XML files that supports rich features like formatting, images, and tables. |
| PDF |
PDF format, pdf file, Portable Document Format |
A format that is used to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. |
| PNG |
PNG format, png file, Portable Network Graphics |
A format that is a raster-graphics file format that supports lossless data compression. |
| tar |
.tar file, tarball |
A format that is an archive file format for bundling multiple files and directories into a single file, often on Unix-like systems, to simplify backups and distribution. |
| gb |
gb format, gb file, GenBank format |
A format that is a standard plain-text format used for storing biological sequence information, such as DNA, RNA and protein sequences, along with associated metadata. |
| jpg |
jpg format, jpg file, JPEG format, JPEG |
A format that is a type of image format that is saved using the method of lossy compression. |
| directory |
folder, directory folder |
A "directory file format" isn't one standard, but refers to the underlying file system's internal structure that organizes files and other directories, containing entries like inode numbers and names in Unix-like systems, or a similar mapping structure in others like FAT or NTFS. Directories, also known as folders, are special files themselves that store lists of pointers to other files and directories, enabling a hierarchical, tree-like structure for organizing data on a storage device. |
| bmp |
bmp format, bmp file, bitmap |
A format that is a raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). |
| fasta |
FASTA format, fasta file |
A format that 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. |
| gz |
gz format, gz file, gzip format, gzip |
A format that is a compressed archive created using the standard gzip (GNU zip) compression algorithm. A GZ File may contain multiple compressed files, directories and file stubs. |
| javascript |
JS, JS format, js file, JavaScript |
A format that contains JavaScript code for execution on web pages. JavaScript files are stored with the .js extension. |
| svg |
SVG format, svg file, Scalable Vector Graphics |
A format that uses XML based text format for describing the appearance of an image (Scalar Vector Graphics file). |
| txt |
TXT format, txt file, text file, flat file |
A format that is structured as a sequence of lines of electronic text. |
| parquet |
parquet format, parquet file, Apache Parquet |
A format that is a free and open-source column-oriented data storage format in the Apache Hadoop ecosystem. |
| zip |
zip format, zip file |
A format (archive file format) that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. |
| xlsx |
XLSX format, xlsx file, Microsoft Excel Open XML Spreadsheet |
A format that is a modern Microsoft Excel spreadsheet format that uses Office Open XML (OOXML), a zipped archive of XML files that supports rich features like formatting, formulas, and charts. |