FASTQ to FASTA converter

How to convert FASTQ to FASTA?

The easiest way to convert FASTQ to FASTA format online is to use this ProteinIQ FASTQ to FASTA converter. To convert FASTQ to FASTA, paste FASTQ records or upload a .fastq, .fq, or .txt file, choose any read filters you need, and run the converter. ProteinIQ validates the FASTQ records, removes quality-score lines, preserves read headers and sequence case by default, and returns a .fasta file.

For one FASTQ record:

@read_1 sample
ACGTRYSWKM
+
IIIIIIIIII

The FASTA output contains the same read identifier and sequence, without the + separator or quality string:

>read_1 sample
ACGTRYSWKM

For multiple FASTQ records, each read becomes a separate FASTA record:

>read_1
ACGTACGT
>read_2
TTGGAACC

The converter also supports wrapped FASTQ records where the sequence or quality section spans multiple lines. The total number of quality characters must match the total sequence length after wrapping is joined.

Results

The converter produces FASTA-formatted output that can be copied to clipboard or downloaded as a .fasta file. A summary file is also returned so filtering decisions are auditable.

How FASTQ to FASTA conversion works

FASTQ records contain four logical sections:

• Header: Starts with @ and contains the read identifier plus optional description.
• Sequence: Contains nucleotide letters. ProteinIQ accepts DNA and RNA bases plus IUPAC ambiguity symbols: A, C, G, T, U, R, Y, S, W, K, M, B, D, H, V, and N.
• Separator: Starts with +. It may be a bare + or repeat the read identifier.
• Quality: Contains one ASCII quality character per sequence letter.

The converter reads each FASTQ record, joins wrapped sequence and quality sections, checks that the sequence and quality lengths match, applies optional trimming and filters, then writes each passing read as FASTA.

Malformed records are rejected instead of being silently skipped. Common validation errors include missing @ headers, missing + separator lines, sequence and quality lengths that do not match, and sequence characters outside the supported nucleotide alphabet.

FASTQ to FASTA filtering rules

Filtering is optional. With the default No filtering setting, every valid read is converted.

Quality filtering uses average read quality after optional end trimming. For example, Q20+ keeps reads with an average score of at least 20. The selected quality encoding matters because the same ASCII character can represent different quality scores in Phred+33, Phred+64, and Solexa+64 files.

Length filtering runs after optional trimming. If Trim low-quality ends is enabled, bases below the trim threshold are removed from the start and end of the read first, then the post-trimming length is compared with the minimum and maximum length settings.

Remove reads containing N excludes reads with unknown N bases. Other IUPAC ambiguity symbols such as R, Y, S, and W remain valid because they can represent known ambiguity rather than an unknown base.

FASTA output rules

FASTA output is simple, but a few rules matter for downstream compatibility.

• Header line: Each converted read starts with >, followed by the FASTQ header without the leading @.
• Sequence line: The sequence is written below the header and wrapped at 80 characters per line.
• Quality scores removed: FASTA cannot store per-base quality characters. Keep the original FASTQ file if quality scores may be needed later.
• Case preservation: Sequence letter case is preserved by default. Lowercase FASTQ sequence letters remain lowercase in the FASTA output.
• Optional quality header: When Add average quality to headers is enabled, the read's average quality is appended to the FASTA header.

Which FASTA converter should I use?

Use FASTQ to FASTA when your input is sequencing-read data with quality-score lines. Use a different converter when the source file is not valid FASTQ.

FAQ

How do I convert a FASTQ file to FASTA format?

Upload the .fastq or .fq file, keep Quality threshold set to No filtering unless you want to remove low-quality reads, and run the converter. The result can be copied or downloaded as a .fasta file.

Does FASTQ to FASTA keep quality scores?

No. FASTA does not have a field for per-base quality scores. This converter can append each read's average quality to the FASTA header, but the original per-base quality string is removed from the FASTA output.

Can FASTQ records be wrapped across multiple lines?

Yes. The sequence and quality sections can span multiple lines as long as the joined quality string has exactly one character per joined sequence letter.

Which quality encoding should I choose?

Use Phred+33 for most modern FASTQ files, including Sanger and Illumina 1.8+ data. Use Phred+64 for older Illumina files and Solexa+64 for early Solexa-format reads. If the source is unknown and the file is modern, Phred+33 is usually the correct choice.

Should I use FASTQ to FASTA or TXT to FASTA?

Use FASTQ to FASTA when your input has @ headers, + separator lines, and quality strings. Use TXT to FASTA for raw sequence text copied from notes, spreadsheets, reports, or plain text files.