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

By Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, Peter M. Rice. Nucleic Acids Research, 2009

1,806 citations recorded by the source corpus.

FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1221de833f4909b7bc27790fa0cd080d756d8982

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

PANDAseq: paired-end assembler for illumina sequences (2012, background): “[7] Assuming all nucleotides are equally likely (i.”
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis (2013, methodology): “These colorimetric signals are translated into base calls by an internal Illumina software (CASAVA), represented in the FASTQ format [13], where each nucleotide is associated to an ASCII-encoded quality number corresponding to a PHRED score (Q) [14], which is directly translated into the probability”
Using the Velvet de novo assembler for short-read sequencing technologies (2010, methodology): “This spurred the development of another category of assemblers, based on the use of the de Bruijn graph, among which are EULER (Pevzner et al., 2001; Chaisson et al., 2009), ALLPATHS (Butler et al., 2008), ABySS (Simpson et al., 2009), SOAPdenovo (Li et al., 2010), and Velvet (Zerbino and Birney,…”
The Sequence Read Archive (2010, methodology): “Before next-generation sequencing platforms existed, the most commonly used format for the representation of base calls and quality scores was the Sanger Fastq format (6).”
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species (2015, methodology): “Data pre-processing An overall quality of the MiSeq reads was evaluated by the programs FASTQC (available from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and SUGAR [24].”
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets (2011, neutral): “data) [53] using the web interface.”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, methodology): “For the 32-genome E. coli dataset, Parsnp ’ s output totals just 4.5 MB, compared to 13 GB required to store compressed FASTQ [100] and VCF [101] files and 149 MB to store XMFA [38].”
Scaling read aligners to hundreds of threads on general-purpose processors (2017, background): “FASTQ reads [16]) or writing output (SAM [31] alignments).”
BayesHammer: Bayesian clustering for error correction in single-cell sequencing (2012, background): “Notice that in practice, the fastq file format [11] contains characters that encode probabilities on a logarithmic scale (in particular, products of probabilities used below correspond to sums of actual quality values).”
PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2013, neutral): “In paired-end sequencing mode, the Illumina Consensus Assessment of Sequence and Variation (CASAVA) software generates two FASTQ files (Cock et al. , 2010), one for each reading direction of the fragment.”
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, methodology): “The following options are of particular importance, and failing to set them to appropriate values will lead to unexpected results: options:Qualityoffset : The ASCII value used to encode the Phred scores in the input FASTQ reads 77 .”