awesome-bioinformatics-formats
Curated list of bioinformatics formats and publications
https://github.com/kmhernan/awesome-bioinformatics-formats
Last synced: 2 days ago
JSON representation
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EDAM
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Formats
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General
- HDF5 - [[edam:format_3590](http://edamontology.org/format_3590)] HDF5 is a data model, library, and file format for storing and managing data.
- tiledb - TileDB manages massive dense and sparse multi-dimensional array data that frequently arise in important scientific applications.
- NetCDF - [[edam:format_3650](http://edamontology.org/format_3650)] Network Common Data Form is a set of interfaces for array-oriented data access and a freely distributed collection of data access libraries for C, Fortran, C++, Java, and other languages.
- SQLite - [[edam:format_3621](http://edamontology.org/format_3621)] SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
- tiledb - TileDB manages massive dense and sparse multi-dimensional array data that frequently arise in important scientific applications.
- NetCDF - [[edam:format_3650](http://edamontology.org/format_3650)] Network Common Data Form is a set of interfaces for array-oriented data access and a freely distributed collection of data access libraries for C, Fortran, C++, Java, and other languages.
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Genomic Intervals
- segmentation file - A tab-delimited text file that lists loci and associated numeric values associated with copy number.
- bedGraph - [[edam:format_3583](http://edamontology.org/format_3583)] The bedGraph format allows display of continuous-valued data in track format.
- bigBed - [[edam:format_3004](http://edamontology.org/format_3004)] Binary and indexed form of [BED](https://genome.ucsc.edu/FAQ/FAQformat.html#format1).
- interval list - The intervals are given in the form `<chr> <start> <stop> + <target_name>`, with fields separated by tabs, and the coordinates are 1-based (first position in the genome is position 1, not position 0).
- segmentation file - A tab-delimited text file that lists loci and associated numeric values associated with copy number.
- tabix - [[edam:format_3616](http://edamontology.org/format_3616)] An *index* file format for genomic intervals (can be used on bed, gtf, vcf, etc).
- interval list - The intervals are given in the form `<chr> <start> <stop> + <target_name>`, with fields separated by tabs, and the coordinates are 1-based (first position in the genome is position 1, not position 0).
- tabix - [[edam:format_3616](http://edamontology.org/format_3616)] An *index* file format for genomic intervals (can be used on bed, gtf, vcf, etc).
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Genomic Features
- GFF2 - [[edam:format_1974](http://edamontology.org/format_1974)] The general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences version 2.
- GFF3 - [[edam:format_1975](http://edamontology.org/format_1975)] The general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences version 3.
- genePred - [[edam:format_3011](http://edamontology.org/format_3011)] a table format commonly used for gene prediction tracks.
- GFF2 - [[edam:format_1974](http://edamontology.org/format_1974)] The general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences version 2.
- GFF3 - [[edam:format_1975](http://edamontology.org/format_1975)] The general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences version 3.
- GTF - [[edam:format_2306](http://edamontology.org/format_2306)] GTF stands for Gene transfer format. It borrows from [GFF2](http://gmod.org/wiki/GFF2), but has additional structure that warrants a separate definition and format name.
- genePred - [[edam:format_3011](http://edamontology.org/format_3011)] a table format commonly used for gene prediction tracks.
- GTF - [[edam:format_2306](http://edamontology.org/format_2306)] GTF stands for Gene transfer format. It borrows from [GFF2](http://gmod.org/wiki/GFF2), but has additional structure that warrants a separate definition and format name.
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Genotype Data
- MAF - A Mutation Annotation Format (MAF) file (.maf) is a tab-delimited text file that lists mutations.
- oxford-bgen - Binary version of the native [Oxford gen format](https://www.cog-genomics.org/plink2/formats#gen). Operations on bgen files are generally faster and more descriptive than on plain gen files, and the file size of bgen files is also smaller -- UK Biobank genotypes are in bgen format. Latest bgen version is 1.3.
- pileup - [[edam:format_3015](http://edamontology.org/format_3015)] Describes the base-pair information at each chromosomal position. This format facilitates SNP/indel calling and brief alignment viewing by eyes.
- GDS - Genomic Data Structure is a storage format for bioinformatics data similar to [NetCDF](https://www.unidata.ucar.edu/software/netcdf/).
- BCF - [[edam:format_3020](http://edamontology.org/format_3020)] Binary and compressed [VCF](http://samtools.github.io/hts-specs/VCFv4.3.pdf) format.
- GVF - [[edam:format_3019](http://edamontology.org/format_3019)] The Genome Variation Format (GVF) is a very simple file format for describing sequence_alteration features at nucleotide resolution relative to a reference genome.
- oxford-bgen - Binary version of the native [Oxford gen format](https://www.cog-genomics.org/plink2/formats#gen). Operations on bgen files are generally faster and more descriptive than on plain gen files, and the file size of bgen files is also smaller -- UK Biobank genotypes are in bgen format. Latest bgen version is 1.3.
- pileup - [[edam:format_3015](http://edamontology.org/format_3015)] Describes the base-pair information at each chromosomal position. This format facilitates SNP/indel calling and brief alignment viewing by eyes.
- plink2-pgen - PLINK2 binary genotype table capable of representing mixed-phase, multiallelic, and mixed-hardcall/dosage/missing genotype data.
- VCF - [[edam:format_3016](http://edamontology.org/format_3016)] Variant Call Format.
- plink-ped - [[edam:format_3288](http://edamontology.org/format_3288)] PLINK plain-text genotype format. Mostly has been replaced by bed/bim/fam, but is useful if someone wants to actually look at the SNPs in plain-text since Plink bed is in binary, and also wants to retain more information than from a VCF (eg. additional individual information).
- BCF - [[edam:format_3020](http://edamontology.org/format_3020)] Binary and compressed [VCF](http://samtools.github.io/hts-specs/VCFv4.3.pdf) format.
- VCF - [[edam:format_3016](http://edamontology.org/format_3016)] Variant Call Format.
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Molecular Structural Data
- CTfile - The CTfile Formats document fully describes the formats for CTfiles (chemical table files) including: Molfiles, RGfiles, Rxnfiles, SDfiles, RDfiles, XDfiles.
- mmCIF - [[edam:format_1477](http://edamontology.org/format_1477)] Another format for PDB molecular structures.
- CTfile - The CTfile Formats document fully describes the formats for CTfiles (chemical table files) including: Molfiles, RGfiles, Rxnfiles, SDfiles, RDfiles, XDfiles.
- mmCIF - [[edam:format_1477](http://edamontology.org/format_1477)] Another format for PDB molecular structures.
- PDB - [[edam:format_1476](http://edamontology.org/format_1476)] The Protein Data Bank (PDB) format provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. This representation was created in the 1970's and a large amount of software using it has been written.
- PDB - [[edam:format_1476](http://edamontology.org/format_1476)] The Protein Data Bank (PDB) format provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. This representation was created in the 1970's and a large amount of software using it has been written.
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Medical Imaging Data
- DICOM - [[edam:format_3548](http://edamontology.org/format_3548)] Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
- NifTI - [[edam:format_3549](http://edamontology.org/format_3549)] Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
- DICOM - [[edam:format_3548](http://edamontology.org/format_3548)] Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
- NifTI - [[edam:format_3549](http://edamontology.org/format_3549)] Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
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Dense Genomic Data
- bigWig - [[edam:format_3006](http://edamontology.org/format_3006)] The bigWig format is useful for dense, continuous data and is a binary form of [wiggle](https://genome.ucsc.edu/goldenPath/help/wiggle.html).
- Genomedata - a format for efficient storage of multiple tracks of numeric data anchored to a genome.
- GenomicsDB - GenomicsDB is an open sourced library and tools with a focus on optimizing sparse array storage specifically for genomic data.
- wiggle - [[edam:format_3005](http://edamontology.org/format_3005)] ASCII format for dense, continuous data.
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Unaligned Sequencing Data
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Aligned Sequencing Data
- CALF - The Compact ALignment Format records the base qualities and mapping qualities of the aligned reads, and unaligned reads data.
- CRAM - [[edam:format_3462](http://edamontology.org/format_3462)] Further lossless compression of [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf) format.
- MAF - [[edam:format_3008](http://edamontology.org/format_3008)] The multiple alignment format stores a series of multiple alignments in a format that is easy to parse and relatively easy to read.
- SAM - [[edam:format_2573](http://edamontology.org/format_2573)] The Sequence Alignment/Map format.
- BAM - [[edam:format_2572](http://edamontology.org/format_2572)] Binary [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf) format. _note: it is becoming more common to store unaligned reads in a BAM called a uBAM_
- CALF - The Compact ALignment Format records the base qualities and mapping qualities of the aligned reads, and unaligned reads data.
- CRAM - [[edam:format_3462](http://edamontology.org/format_3462)] Further lossless compression of [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf) format.
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Miscellaneous
- BIOM - [[edam:format_3746](http://edamontology.org/format_3746)] The Biological Observation Matrix (BIOM) file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
- Pairs - The specification for the text contact list file format for chromosome conformation experiments (e.g., Hi-C).
- SBML - [[edam:format_2585](http://edamontology.org/format_2585)] Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
- SBML - [[edam:format_2585](http://edamontology.org/format_2585)] Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
- BIOM - [[edam:format_3746](http://edamontology.org/format_3746)] The Biological Observation Matrix (BIOM) file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
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Review Papers and Blogs