Data

What is FASTQ?

FASTQ is a widely used text format that pairs sequencer read sequences with per-base quality scores. A common record has an identifier beginning with `@`, a sequence, a `+` separator, and a quality string whose length matches the sequence. FASTQ has no single formal specification, and incompatible quality encodings exist, including Sanger Phred+33 and historical Solexa/Illumina variants. Files commonly use `.fastq` or `.fq` and may be externally compressed, for example with gzip. FASTQ usually stores reads before alignment; it does not serve the same role as SAM/BAM alignment records with reference positions.

.fastq · .fq · .fastq.gz · .fq.gzBase sequences and quality scores

Basic information

Extension: .fastq / .fq
Compression: Optional external compression, often .gz
Category: Data

When to choose this format

Keeping read identifiers, sequences, and corresponding base qualities together
Submitting read data to archives such as NCBI SRA

When to avoid this format

Recording alignment positions on a reference genome
Storing only a reference or assembled sequence without quality values

Common uses

Passing sequencing reads and per-base quality scores between analysis steps
Storing unaligned reads, including paired-end data, before downstream analysis

Features

Associates each sequencing read with a quality value for each base
A common four-line representation uses an `@` identifier, sequence, `+` line, and quality string
Quality scores such as Phred are encoded as ASCII using different offsets and score systems
Paired-end reads may be stored in matching files or interleaved

Advantages and disadvantages

Advantages

Keeps sequences and qualities together for many sequencing tools and archives
Text is compressible and widely used to exchange reads across instruments and pipeline stages
Headers can carry read identifiers and platform-specific information

Disadvantages

Quality-encoding variants are not interchangeable, and the offset cannot be reliably inferred from characters alone
Text files can be large and require suitable parsers and compression support
It does not by itself describe alignments, reference coordinates, variant calls, or full sample metadata

Open and convert

How to open

Use a sequencing tool that supports the file's FASTQ variant. Check the `@` identifier, sequence and quality lengths, `+` line, quality scheme such as Phred+33 or Phred+64, and the instrument or pipeline documentation. For paired-end data, verify read order and identifiers across both files. Read gzip-compressed files with a compatible tool or decompress them.

How to convert

To change quality encoding, identify the original Phred or Solexa score system and ASCII offset, decode numeric scores correctly, then re-encode them. Exporting only sequences to FASTA discards quality values. Producing aligned SAM/BAM data is a separate mapping workflow using a reference and analysis software, not a filename change.

Cautions

Phred+33 and historical Phred+64/Solexa encodings assign different meanings to quality characters. Do not infer the scheme from a filename or character range alone; consult instrument, software, or dataset documentation.
Paired-end files must retain read order and identifier/read-number correspondence. Validate them against the receiving pipeline's rules.
FASTQ may contain human genetic data, pathogen or research sequences, and sample identifiers. Review privacy, consent, research ethics, and access controls before sharing.
Some tools handle multiline records or platform-specific headers beyond the common four-line layout. Check the variant expected by your parser and archive.

FAQ

How is FASTQ different from FASTA?

FASTQ associates per-base quality scores with a sequence. FASTA usually stores an identifier and sequence but no quality values.

Do all FASTQ files use the same quality encoding?

No. Phred+33 is widely used, but historical Phred+64 and Solexa variants exist. Confirm the producer and score scheme.

Is FASTQ aligned data?

Usually not. FASTQ stores reads and quality scores; mapping positions on a reference are represented in alignment formats such as SAM, BAM, or CRAM.

Related formats

SAMSAM (Sequence Alignment/Map) is a tab-delimited text format for sequencing reads and their alignment to reference sequences. Optional header lines describe references and software; each alignment record carries a read name, FLAG, reference and position, MAPQ, CIGAR, sequence, quality, and optional tags. The specification can also represent unmapped reads, so not every record is necessarily aligned. SAM is easy to inspect but can be large; BAM is its binary representation and CRAM adds reference-aware compression.BAMBAM (Binary Alignment/Map) is the binary representation of SAM alignment data defined by the SAMv1 specification. BAM is normally compressed in BGZF blocks; this block structure supports indexed access to regions. It can store reference headers, read names, FLAG, CIGAR, positions, sequence qualities, and tags, and may include unmapped reads. Coordinate-sorted BAM can be paired with an index such as BAI or CSI. BAM is suited to machine processing, but not direct reading; reference identity and index consistency matter.CRAMCRAM stores sequencing reads and alignments using encodings that can exploit differences from a reference sequence, often achieving greater compression than BAM. The specification supports both lossless and lossy preservation strategies and does not prescribe which data must be retained. A .cram extension alone therefore cannot confirm whether base qualities or tags were preserved; check the creating tool and settings. Some files or workflows need an exact external reference to decode, while references can also be embedded. CRAI indexes support regional access.GZIPGZIP compresses data losslessly. A .gz file commonly wraps one file; tar.gz first groups files with tar and then compresses that archive.FASTAFASTA is a text format with a definition line starting with > followed by sequence data. This article covers nucleotide and reference sequences. FASTA alone contains no per-base quality scores.