FASTQ to FASTA converter

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Convert strict FASTQ records to FASTA by preserving read identifiers and sequences while removing quality scores.

Input
Expects strict FASTQ (4-line records). Converts by dropping quality lines.
FASTQ input. Processed synchronously.
Output formatting
Limits: up to 10 MB (uncompressed) • up to 200,000 records

About this tool

Converts strict FASTQ files to FASTA format by preserving the read header and sequence, and dropping the quality scores. This conversion is commonly used before tools such as BLAST or sequence alignment methods that accept FASTA input but ignore per-base quality information. Basic FASTQ structure is validated (4-line records, “+” separator, and matching sequence/quality lengths) to ensure safe conversion.

For comprehensive FASTA/FASTQ validation — including header rules, alphabet checks, and quality character ranges — use the FASTA/FASTQ Validator. Format rules and examples are documented in the FASTA/FASTQ formats reference.

Tool guarantees
  • ✓ No hidden transformations or guessing
  • ✓ Input processed once and not stored
  • ✓ FASTQ structure validated (strict)

Results

Submit input to see results here.

  • FASTQ: 4-line records: “@header”, sequence, “+”, quality.
  • Conversion: outputs FASTA headers (“>…”) and sequence lines; quality is discarded.
  • Validation: this tool requires strict FASTQ structure and matching sequence/quality lengths.

  • Downstream tools: provide FASTA when quality scores are not needed.
  • Debugging: quickly inspect sequences without FASTQ noise.
  • Filtered subsets: convert trimmed, unmapped, or diagnostic FASTQ subsets to FASTA.
  • Small conversions: quick, deterministic format conversion for limited inputs.

FASTQ files store both sequences and per-base quality scores. Many downstream tools only require the sequence itself and accept FASTA input. Converting FASTQ to FASTA is therefore common after filtering, trimming, or subsetting reads, when quality scores are no longer needed.