FASTA/FASTQ Format Inspector

The Languages of Sequence Data

Before you can align, assemble, or analyse a genome, you need to read the data. FASTA and FASTQ are the two most common file formats in bioinformatics — nearly every sequencing instrument, database, and analysis tool reads or writes one of them. Understanding their structure is a prerequisite for debugging pipelines, writing parsers, and catching data corruption.

This simulation lets you paste or upload a file and see its anatomy highlighted byte by byte.

What You’ll Explore

• FASTA anatomy. Each record starts with a header line beginning with >, followed by one or more lines of sequence. The header typically contains an identifier and an optional description separated by a space. There is no formal specification for what goes in the header — different tools and databases use different conventions.
• FASTQ anatomy. Each record has exactly four lines: a header starting with @, a sequence line, a separator line starting with +, and a quality line. The quality line encodes a per-base quality score as an ASCII character. Each character maps to a Phred score: Q = −10 log₁₀(P), where P is the probability that the base call is wrong.
• Quality score encoding. Toggle between Phred+33 (Sanger/Illumina 1.8+) and Phred+64 (older Illumina) and see how the same ASCII characters map to different quality values. A Phred score of 30 means a 1 in 1,000 chance of error; 40 means 1 in 10,000.
• Validate a file. The inspector checks for common problems: inconsistent line lengths, invalid characters in the sequence, quality lines that don’t match the sequence length, and mixed line endings.

Key Concepts

FASTA Format

FASTA is the simpler of the two formats. A minimal record looks like this:

>seq1 Human hemoglobin alpha
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH

Sequences can span multiple lines (typically wrapped at 60 or 80 characters). Multi-FASTA files contain multiple records concatenated together. The format is used for both nucleotide and protein sequences — the alphabet is the only difference.

FASTQ Format

FASTQ extends FASTA by adding per-base quality scores. A single record:

@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

The + line can optionally repeat the sequence identifier but is usually left bare. The quality string must be exactly the same length as the sequence string.

Phred Quality Scores

Phred scores are the universal language of base-call confidence. The mapping is logarithmic:

Modern Illumina instruments typically produce reads with average Phred scores between 30 and 40. Long-read platforms (PacBio HiFi, Oxford Nanopore) have different error profiles and quality distributions.

Background Reading

1. Cock, P. J. A. et al. (2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6), 1767–1771.