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https://github.com/kmhernan/awesome-bioinformatics-formats

Curated list of bioinformatics formats and publications
https://github.com/kmhernan/awesome-bioinformatics-formats

List: awesome-bioinformatics-formats

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Curated list of bioinformatics formats and publications

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# awesome-bioinformatics-formats

Curated list of bioinformatics formats and publications. Not every format here is "awesome" per se, but if you are

thinking about creating a new format this could be your first place to look at potential pre-existing formats. We also

include formats not specific to bioinformatics, but should be considered for bioinformatics applications.



Please feel free to [contribute](https://github.com/kmhernan/awesome-bioinformatics-formats/blob/master/CONTRIBUTING.md).



## EDAM



> EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of concepts with preferred terms and synonyms, definitions, and some additional information - organised into a simple and intuitive hierarchy for convenient use.



[EDAM](http://edamontology.org/page) is a more exhaustive and established ontology for bioinformatics data 

including formats. This is not intended to be a replacement or contain as much information as EDAM, please refer

to their great resources including this [explorable ontology](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2350)

for more information. We ask that where possible you link to the EDAM ontology for any formats your contribute. If your

format is not available, then it is a great opportunity to contribute to EDAM as well.



# Table of Contents



- [Formats](#formats)

  - [General](#general)

  - [Dense Genomic Data](#dense-genomic-data)

  - [Genomic Intervals](#genomic-intervals)

  - [Genomic Features](#genomic-features)

  - [Genotype Data](#genotype-data)

  - [Unaligned Sequencing Data](#unaligned-sequencing-data)

  - [Aligned Sequencing Data](#aligned-sequencing-data)

  - [Molecular Structural Data](#molecular-structural-data)

  - [Medical Imaging Data](#medical-imaging-data)

  - [Miscellaneous](#miscellaneous)

- [Review Papers and Blogs](#review-papers-and-blogs)

- [License](#license)



----



## Formats



### General



Formats not specific to bioinformatics that should be considered.



* [HDF5](https://portal.hdfgroup.org/display/support) - [[edam:format_3590](http://edamontology.org/format_3590)] HDF5 is a data model, library, and file format for storing and managing data.

* [NetCDF](https://www.unidata.ucar.edu/software/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](https://sqlite.org/index.html) - [[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](https://tiledb.io/) - TileDB manages massive dense and sparse multi-dimensional array data that frequently arise in important scientific applications.



### Dense Genomic Data



Formats associated with storing dense functional genomics data.



* [bigWig](https://genome.ucsc.edu/goldenPath/help/bigWig.html) - [[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](https://academic.oup.com/bioinformatics/article/26/11/1458/203307) - a format for efficient storage of multiple tracks of numeric data anchored to a genome.

* [GenomicsDB](https://www.genomicsdb.org/) - GenomicsDB is an open sourced library and tools with a focus on optimizing sparse array storage specifically for genomic data.

* [wiggle](https://genome.ucsc.edu/goldenPath/help/wiggle.html) - [[edam:format_3005](http://edamontology.org/format_3005)] ASCII format for dense, continuous data.



### Genomic Intervals



Formats associated with storing genomic intervals (e.g., contig, start, stop, strand).



* [BED](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - [[edam:format_3003](http://edamontology.org/format_3003)] Browser Extensible Data format provides a flexible way to define the data lines that are displayed in an annotation track.

* [bedGraph](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) - [[edam:format_3583](http://edamontology.org/format_3583)] The bedGraph format allows display of continuous-valued data in track format.

* [bigBed](https://genome.ucsc.edu/goldenPath/help/bigBed.html) - [[edam:format_3004](http://edamontology.org/format_3004)] Binary and indexed form of [BED](https://genome.ucsc.edu/FAQ/FAQformat.html#format1).

* [interval list](https://gatkforums.broadinstitute.org/gatk/discussion/1319/collected-faqs-about-interval-lists) - The intervals are given in the form `   + `, with fields separated by tabs, and the coordinates are 1-based (first position in the genome is position 1, not position 0).

* [narrowPeak](https://genome.ucsc.edu/FAQ/FAQformat.html#format12) - [[edam:format_3613](http://edamontology.org/format_3613)] This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.

* [segmentation file](https://software.broadinstitute.org/software/igv/SEG) - A tab-delimited text file that lists loci and associated numeric values associated with copy number.

* [tabix](http://samtools.github.io/hts-specs/tabix.pdf) - [[edam:format_3616](http://edamontology.org/format_3616)] An *index* file format for genomic intervals (can be used on bed, gtf, vcf, etc).



### Genomic Features



Formats for describing genomic features (e.g., gene models, etc.).



* [genePred](http://genome.ucsc.edu/FAQ/FAQformat#format9) - [[edam:format_3011](http://edamontology.org/format_3011)] a table format commonly used for gene prediction tracks.

* [GFF2](http://gmod.org/wiki/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](http://gmod.org/wiki/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](http://mblab.wustl.edu/GTF22.html) - [[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.



### Genotype Data



Formats associated with genotype data.



* [BCF](http://samtools.github.io/hts-specs/BCFv2_qref.pdf) - [[edam:format_3020](http://edamontology.org/format_3020)] Binary and compressed [VCF](http://samtools.github.io/hts-specs/VCFv4.3.pdf) format.

* [GDS](http://corearray.sourceforge.net/) - Genomic Data Structure is a storage format for bioinformatics data similar to [NetCDF](https://www.unidata.ucar.edu/software/netcdf/). 

* [GVF](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md) - [[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.

* [MAF](https://software.broadinstitute.org/software/igv/MutationAnnotationFormat) - A Mutation Annotation Format (MAF) file (.maf) is a tab-delimited text file that lists mutations.

* [oxford-bgen](https://www.well.ox.ac.uk/~gav/bgen_format/index.html) - 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.

* [oxford-gen](https://www.cog-genomics.org/plink2/formats#gen) - [[edam:format_3812](http://edamontology.org/format_3812)] Native text genotype file format for Oxford statistical genetics tools, such as IMPUTE2 and SNPTEST.

* [pileup](http://samtools.sourceforge.net/pileup.shtml) - [[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.

* [plink-bed](https://www.cog-genomics.org/plink2/formats#bed) - PLINK binary biallelic genotype table.

* [plink-ped](https://www.cog-genomics.org/plink2/formats#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).

* [plink2-pgen](https://www.cog-genomics.org/plink/2.0/formats#pgen) - PLINK2 binary genotype table capable of representing mixed-phase, multiallelic, and mixed-hardcall/dosage/missing genotype data.

* [VCF](http://samtools.github.io/hts-specs/VCFv4.3.pdf) - [[edam:format_3016](http://edamontology.org/format_3016)] Variant Call Format.



### Unaligned Sequencing Data



Formats associated with storing unaligned sequencing data.



* [FASTA](https://en.wikipedia.org/wiki/FASTA_format) - [[edam:format_1929](http://edamontology.org/format_1929)] ASCII format for storing nucleotide/amino acid sequences.

* [FASTQ](https://academic.oup.com/nar/article/38/6/1767/3112533) - [[edam:format_1930](http://edamontology.org/format_1930)] Designed as a replacement for FASTA, combining the sequence and quality information in the same file.



### Aligned Sequencing Data



Formats associated with storing aligned sequencing data.



* [BAM](http://samtools.github.io/hts-specs/SAMv1.pdf) - [[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](http://www.phrap.org/phredphrap/calf.pdf) - The Compact ALignment Format records the base qualities and mapping qualities of the aligned reads, and unaligned reads data.

* [CRAM](http://samtools.github.io/hts-specs/CRAMv3.pdf) - [[edam:format_3462](http://edamontology.org/format_3462)] Further lossless compression of [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf) format.

* [MAF](https://genome.ucsc.edu/FAQ/FAQformat.html#format5) - [[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](http://samtools.github.io/hts-specs/SAMv1.pdf) - [[edam:format_2573](http://edamontology.org/format_2573)] The Sequence Alignment/Map format.



### Molecular Structural Data



* [CTfile](http://www.3dsbiovia.com/products/collaborative-science/biovia-draw/ctfile-no-fee.html) - The CTfile Formats document fully describes the formats for CTfiles (chemical table files) including: Molfiles, RGfiles, Rxnfiles, SDfiles, RDfiles, XDfiles.

* [mmCIF](http://mmcif.wwpdb.org/) - [[edam:format_1477](http://edamontology.org/format_1477)] Another format for PDB molecular structures.

* [PDB](http://www.wwpdb.org/documentation/file-format) - [[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. 



### Medical Imaging Data



Formats associated with medical imaging data.



* [DICOM](http://dicom.nema.org/) - [[edam:format_3548](http://edamontology.org/format_3548)] Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.

* [NifTI](http://nifti.nimh.nih.gov/nifti-1) - [[edam:format_3549](http://edamontology.org/format_3549)] Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.



### Miscellaneous 



Formats that currently don't have a good section to place them yet (but still very relevant).



* [BIOM](http://biom-format.org/) - [[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](https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md) - The specification for the text contact list file format for chromosome conformation experiments (e.g., Hi-C).

* [SBML](http://sbml.org/Basic_Introduction_to_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. 



## Review Papers and Blogs



This section contains links to relevant review papers and blog posts about bioinformatics formats.



* [hts-specs](http://samtools.github.io/hts-specs/) - Specs from HTS



## License



[![CC0](http://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg)](https://creativecommons.org/publicdomain/zero/1.0/)