Convert standard FASTQ reads to FASTA with validation, IUPAC nucleotide support, average-quality filtering, and downloadable summaries
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
Convert GenBank files to FASTA format
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
Convert DNA sequences to RNA (transcription) - replaces T with U
Convert RNA sequences to DNA (reverse transcription) - replaces U with T
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
Generate reverse, complement, or reverse-complement of DNA/RNA sequences
Translate DNA sequences to protein sequences using genetic code
Reverse translate protein sequences to possible DNA sequences
Convert standard FASTQ reads to FASTA with validation, IUPAC nucleotide support, average-quality filtering, and downloadable summaries
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
Convert GenBank files to FASTA format
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
Convert DNA sequences to RNA (transcription) - replaces T with U
Convert RNA sequences to DNA (reverse transcription) - replaces U with T
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
Generate reverse, complement, or reverse-complement of DNA/RNA sequences
Translate DNA sequences to protein sequences using genetic code
Reverse translate protein sequences to possible DNA sequences
Configure inputs to begin
Set options on the left, then click “Convert”.
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:
>read_1 sample
ACGTNACGTNThe FASTQ output contains the same identifier and sequence, plus a + separator and one quality character per sequence letter:
@read_1 sample
ACGTNACGTN
+
IIIIIIIIIIFor multiple FASTA records, each sequence becomes a separate FASTQ record:
@read_1
ACGTACGT
+
IIIIIIII
@read_2
TTGGAACC
+
IIIIIIIIFASTA 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. |
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. |
FASTA records contain a header line that starts with > followed by one or more sequence lines. FASTQ records contain four logical sections:
@ and contains the FASTA header without the leading >.+ line.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 |
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 is strict because sequence and quality lengths must match exactly.
@, followed by the FASTA header without the leading >.+.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. |
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.
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.
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.
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.
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.