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FASTA vs FASTQ: sequences and quality retention
FASTA alone stores sequences; FASTQ stores sequences with per-base quality scores.
Which format should you choose?
Use FASTA for reference or assembled sequences and FASTQ for read analysis using quality; retain originals.
Good fit for FASTA
Store reference or assembled nucleotide sequences
- Exchange sequences without requiring quality scores
Good fit for FASTQ
Passing sequencing reads and per-base quality scores between analysis steps · Storing unaligned reads, including paired-end data, before downstream analysis
- Keeping read identifiers, sequences, and corresponding base qualities together
- Submitting read data to archives such as NCBI SRA
Basic information
| Field | FASTA | FASTQ |
|---|---|---|
| Extension | .fasta, .fa | .fastq, .fq, .fastq.gz, .fq.gz |
| MIME type | ||
| Common uses | Store reference or assembled nucleotide sequences | Passing sequencing reads and per-base quality scores between analysis steps · Storing unaligned reads, including paired-end data, before downstream analysis |
| How to open | Use a sequence-aware reader and check duplicate identifiers, symbols and lengths. samtools faidx requires uniform line widths within each sequence except its final line. Rebuild .fai after sequence or newline changes. | 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. |
| Export or convert | Exporting sequence-only FASTA from FASTQ discards quality. FASTA cannot reconstruct original scores. If real QUAL data exist, match identifiers and lengths and confirm the quality scheme before combining. | 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. |
Choose by use case
Exchange sequences without requiring quality scores
Store reference or assembled nucleotide sequences
FASTAKeeping read identifiers, sequences, and corresponding base qualities together
Passing sequencing reads and per-base quality scores between analysis steps · Storing unaligned reads, including paired-end data, before downstream analysis
FASTQSubmitting read data to archives such as NCBI SRA
Passing sequencing reads and per-base quality scores between analysis steps · Storing unaligned reads, including paired-end data, before downstream analysis
FASTQKey point 1
FASTA uses a > definition line followed by sequence.
More on the differencesKey point 2
FASTQ uses @, sequence, a + separator and a matching quality string.
More on the differencesMore on the differences
Decide whether sequence alone suffices or quality-based filtering is needed. Check producer conventions and reader expectations, not just extensions.
- Sequence extraction into FASTA discards original quality. Adding constant scores without real QUAL does not recover measured quality.
- When combining real QUAL, match identifiers, record counts, lengths and quality scheme. Rebuild reference .fai after sequence or newline changes.
Frequently asked questions
Does converting FASTA to FASTQ restore quality?
No. Scores cannot be reconstructed from sequence letters. Combine only genuine original quality data with verified correspondence; do not treat placeholders as measurements.