FAIRsharing is here! From our first incarnation, BioSharing.org, which focussed on the life sciences, we are growing into FAIRsharing.org, to serve users across all disciplines.
Standards > model/format > bsg-s000229


ready FASTQ Sequence and Sequence Quality Format


General Information
FASTQ is a text-based file format for sharing sequencing data combining both the sequence and an associated per base quality score.


Collected/Recommended By



Record updated: Oct. 18, 2016, 10:14 p.m. by The FAIRsharing Team.



Support

No support information provided.


Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

No License Specified.





Connectivity
Related Standards

Terminology Artifacts

No semantic standards defined

Models and Formats


Implementing Databases (16)
GenBank
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.

Aspergillus Genome Database
The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fungal research community.

The DNA Data Bank of Japan
Annotated collection of all publicly available nucleotide and protein sequences. In Japan, DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. Ninety-nine percent of INSD data from Japanese researchers are submitted through DDBJ.

Encyclopedia of DNA Elements at UCSC
Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

modMine
modMine is an integrated web resource of data & tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

RhesusBase
A comprehensive online knowledgebase for the monkey research community.

Mammalian Protein Localization Database
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

Endocrine Pancreas Consortium Database
EPConDB is a resource of the Beta Cell Biology Consortium which displays information about genes expressed in cells of the pancreas and their transcriptional regulation.

Bgee DataBase for Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.

Gramene, a comparative mapping resource for grains
Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species.

European Nucleotide Archive
The European Nucleotide Archive (ENA) is a nucleotide database which is part of an international nucleotide sequence database collaboration. This collaboration comprises ENA itself, the DNA DataBank of Japan (DDBJ), and NCBI GenBank. This resource was formerly called the EMBL nucleotide sequence database. ENA provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.

The European Genome-phenome Archive
The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

EBI Metagenomics
"EBI Metagenomics" is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.

ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

Dog Genome SNP Database
Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog's population, evolution, phenotype and life habit.

Genome Sequence Archive
GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

Scroll for more...


Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

  • This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

Maintains

Undefined

Grant Number(s)

  • BB/D018358/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • BBR/G02264X/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)


Publications

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Cock PJ,Fields CJ,Goto N,Heuer ML,Rice PM
Nucleic Acids Res 2009

View Paper (PubMed) View Paper (DOI)