FASTA to FASTQ Converter

Convert FASTA sequences to FASTQ with configurable mock Phred quality scores.

Input

FASTA input

Score generation method

Output

Configure inputs to begin

Set options on the left, then click “Convert”.

How to convert FASTA to FASTQ?

The easiest way to convert FASTA to FASTQ format online is to use this ProteinIQ FASTA to FASTQ converter. To convert FASTA to FASTQ, paste FASTA records or upload a .fasta, .fa, .fas, .seq, or .txt file, choose a quality score profile, and run the converter. ProteinIQ preserves FASTA headers, generates synthetic Phred+33 quality strings, skips records with invalid sequence characters, and returns a .fastq file.

For one FASTA record:

Text

>read_1 sample
ACGTNACGTN

The FASTQ output contains the same identifier and sequence, plus a + separator and one quality character per sequence letter:

Text

@read_1 sample
ACGTNACGTN
+
IIIIIIIIII

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

Text

@read_1
ACGTACGT
+
IIIIIIII
@read_2
TTGGAACC
+
IIIIIIII

FASTA does not store real base-call confidence, so every quality string generated by this converter is synthetic. Use the output for reference sequences, designed sequences, examples, and pipeline tests. If the original data came from sequencing and real quality scores matter, use the original FASTQ file instead.

Input	Description
`Input`	FASTA text containing one or more sequence records. Accepts pasted text or file uploads. Common extensions: `.fasta`, `.fa`, `.fas`, `.seq`, `.txt`. Maximum file size: 100 MB.

Setting	Description
`Score generation method`	Selects how synthetic quality scores are generated. `High quality (Q40)` is the default. Other options are `Medium quality (Q20)`, `Low quality (Q10)`, `Custom quality score`, `Random scores (Q0-Q40)`, and `Declining quality (Q40 to Q10)`.
`Quality score value (Q0-Q40)`	Custom Phred score used at every position when `Custom quality score` is selected. Values outside Q0-Q40 are clamped to the valid range.

Results

The converter produces FASTQ-formatted output that can be copied to clipboard or downloaded as a .fastq file. A summary file is also returned so skipped records and generated score settings are auditable.

Output	Description
FASTQ file	Converted FASTQ records for valid input sequences.
Conversion summary	Counts total FASTA records, converted records, skipped records, total bases or residues, average converted sequence length, and selected score mode.
FASTQ preview	Rendered FASTQ text for quick inspection before copying or downloading.
Warnings	Notes that quality scores are synthetic and lists skipped records when invalid characters are found.

How FASTA to FASTQ conversion works

FASTA records contain a header line that starts with > followed by one or more sequence lines. FASTQ records contain four logical sections:

Header: Starts with @ and contains the FASTA header without the leading >.
Sequence: Contains the converted sequence in uppercase.
Separator: A + line.
Quality: Contains one ASCII quality character per sequence letter.

ProteinIQ reads each FASTA record, preserves the full header description, validates the sequence, generates a quality string with the selected profile, then writes one FASTQ record for each valid input record. Records with invalid characters are skipped instead of being silently modified.

The converter uses Phred+33 encoding. Each numeric Phred score is converted to a single ASCII character by adding 33 to the score.

Phred score	Error probability	Accuracy	Phred+33 character
Q10	1 in 10	90%	`+`
Q20	1 in 100	99%	`5`
Q30	1 in 1,000	99.9%	`?`
Q40	1 in 10,000	99.99%	`I`

FASTA to FASTQ quality score options

Quality score selection controls how downstream FASTQ-aware tools interpret confidence. The sequence text does not change, but quality-aware filters, trimmers, aligners, and variant workflows may behave differently.

Profile	Generated scores	Use when
`High quality (Q40)`	Q40 at every position	Reference sequences, synthetic constructs, and tests where reads should pass quality filters.
`Medium quality (Q20)`	Q20 at every position	Standard threshold-style test data.
`Low quality (Q10)`	Q10 at every position	Testing low-quality read handling or quality filters.
`Custom quality score`	Selected Q0-Q40 score at every position	Controlled benchmarks that need a specific uniform score.
`Random scores (Q0-Q40)`	Random score at each position	Testing tools that respond to per-position quality variation.
`Declining quality (Q40 to Q10)`	Starts at Q40 and decreases to Q10	Simulating lower quality near the end of each read.

FASTQ output rules

FASTQ output is strict because sequence and quality lengths must match exactly.

Header line: Each converted record starts with @, followed by the FASTA header without the leading >.
Sequence line: The sequence is written in uppercase.
Separator line: The third line is +.
Quality line: The quality string has exactly one Phred+33 character per sequence letter.
Synthetic scores: Generated quality scores do not recover real sequencing confidence.
Skipped records: Invalid records are omitted from the FASTQ file and counted in the conversion summary.

Which FASTQ converter should I use?

Use FASTA to FASTQ when the sequence is already in FASTA format and a downstream tool requires FASTQ input. Use a different converter when the source file already has quality scores or needs sequence cleanup first.

Input format	Best converter	Use when
FASTA sequences needing FASTQ	FASTA to FASTQ	You need synthetic quality strings for FASTA records.
FASTQ sequencing reads	FASTQ to FASTA	You need to remove quality-score lines from read data.
TXT or pasted sequence text	TXT to FASTA	You have raw DNA, RNA, or protein text without FASTA headers.
CSV or spreadsheet-like text	CSV to FASTA	Sequence IDs and sequences are stored in columns.
Generated nucleotide sequences	Random DNA or Random RNA	You need synthetic sequence content before converting or testing.

FAQ

How do I convert a FASTA file to FASTQ format?

Upload the .fasta, .fa, or .fas file, choose a score generation method, and run the converter. The result can be copied or downloaded as a .fastq file.

Does FASTA to FASTQ recover real quality scores?

No. FASTA does not contain per-base quality scores. This converter generates synthetic quality strings so FASTA sequences can be used with tools that require FASTQ input.

Which quality score method should I choose?

Use High quality (Q40) for reference sequences, designed sequences, and compatibility testing. Use Declining quality (Q40 to Q10) or Random scores (Q0-Q40) when testing quality trimming, filtering, or quality-aware algorithms.

Can I convert multiple FASTA records at once?

Yes. Paste or upload a multi-record FASTA file. Each valid FASTA record becomes one FASTQ record, and skipped records are listed in the conversion summary.

Should I use FASTA to FASTQ or TXT to FASTA?

Use FASTA to FASTQ when the input already has FASTA headers that start with >. Use TXT to FASTA for raw sequence text copied from notes, reports, or plain text files.

Related tools

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How to convert FASTA to FASTQ?

For one FASTA record:

Text

>read_1 sample
ACGTNACGTN

The FASTQ output contains the same identifier and sequence, plus a + separator and one quality character per sequence letter:

Text

@read_1 sample
ACGTNACGTN
+
IIIIIIIIII

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

Text

@read_1
ACGTACGT
+
IIIIIIII
@read_2
TTGGAACC
+
IIIIIIII

Input	Description
`Input`	FASTA text containing one or more sequence records. Accepts pasted text or file uploads. Common extensions: `.fasta`, `.fa`, `.fas`, `.seq`, `.txt`. Maximum file size: 100 MB.

Setting	Description
`Score generation method`	Selects how synthetic quality scores are generated. `High quality (Q40)` is the default. Other options are `Medium quality (Q20)`, `Low quality (Q10)`, `Custom quality score`, `Random scores (Q0-Q40)`, and `Declining quality (Q40 to Q10)`.
`Quality score value (Q0-Q40)`	Custom Phred score used at every position when `Custom quality score` is selected. Values outside Q0-Q40 are clamped to the valid range.

Results

Output	Description
FASTQ file	Converted FASTQ records for valid input sequences.
Conversion summary	Counts total FASTA records, converted records, skipped records, total bases or residues, average converted sequence length, and selected score mode.
FASTQ preview	Rendered FASTQ text for quick inspection before copying or downloading.
Warnings	Notes that quality scores are synthetic and lists skipped records when invalid characters are found.

How FASTA to FASTQ conversion works

FASTA records contain a header line that starts with > followed by one or more sequence lines. FASTQ records contain four logical sections:

Header: Starts with @ and contains the FASTA header without the leading >.
Sequence: Contains the converted sequence in uppercase.
Separator: A + line.
Quality: Contains one ASCII quality character per sequence letter.

The converter uses Phred+33 encoding. Each numeric Phred score is converted to a single ASCII character by adding 33 to the score.

Phred score	Error probability	Accuracy	Phred+33 character
Q10	1 in 10	90%	`+`
Q20	1 in 100	99%	`5`
Q30	1 in 1,000	99.9%	`?`
Q40	1 in 10,000	99.99%	`I`

FASTA to FASTQ quality score options

Profile	Generated scores	Use when
`High quality (Q40)`	Q40 at every position	Reference sequences, synthetic constructs, and tests where reads should pass quality filters.
`Medium quality (Q20)`	Q20 at every position	Standard threshold-style test data.
`Low quality (Q10)`	Q10 at every position	Testing low-quality read handling or quality filters.
`Custom quality score`	Selected Q0-Q40 score at every position	Controlled benchmarks that need a specific uniform score.
`Random scores (Q0-Q40)`	Random score at each position	Testing tools that respond to per-position quality variation.
`Declining quality (Q40 to Q10)`	Starts at Q40 and decreases to Q10	Simulating lower quality near the end of each read.

FASTQ output rules

FASTQ output is strict because sequence and quality lengths must match exactly.

Header line: Each converted record starts with @, followed by the FASTA header without the leading >.
Sequence line: The sequence is written in uppercase.
Separator line: The third line is +.
Quality line: The quality string has exactly one Phred+33 character per sequence letter.
Synthetic scores: Generated quality scores do not recover real sequencing confidence.
Skipped records: Invalid records are omitted from the FASTQ file and counted in the conversion summary.

Which FASTQ converter should I use?

Input format	Best converter	Use when
FASTA sequences needing FASTQ	FASTA to FASTQ	You need synthetic quality strings for FASTA records.
FASTQ sequencing reads	FASTQ to FASTA	You need to remove quality-score lines from read data.
TXT or pasted sequence text	TXT to FASTA	You have raw DNA, RNA, or protein text without FASTA headers.
CSV or spreadsheet-like text	CSV to FASTA	Sequence IDs and sequences are stored in columns.
Generated nucleotide sequences	Random DNA or Random RNA	You need synthetic sequence content before converting or testing.

FAQ

How do I convert a FASTA file to FASTQ format?

Upload the .fasta, .fa, or .fas file, choose a score generation method, and run the converter. The result can be copied or downloaded as a .fastq file.

Does FASTA to FASTQ recover real quality scores?

No. FASTA does not contain per-base quality scores. This converter generates synthetic quality strings so FASTA sequences can be used with tools that require FASTQ input.

Which quality score method should I choose?

Can I convert multiple FASTA records at once?

Yes. Paste or upload a multi-record FASTA file. Each valid FASTA record becomes one FASTQ record, and skipped records are listed in the conversion summary.

Should I use FASTA to FASTQ or TXT to FASTA?

Use FASTA to FASTQ when the input already has FASTA headers that start with >. Use TXT to FASTA for raw sequence text copied from notes, reports, or plain text files.