Convert FASTQ sequencing reads to FASTA while preserving headers and sequence case by default. Learn more
Convert FASTQ sequencing reads to FASTA while preserving headers and sequence case by default. Learn more
Convert FASTQ sequencing reads to FASTA while preserving headers and sequence case by default. Learn more
Convert FASTA sequence files to FASTQ format with mock quality scores
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 FASTA sequence files to FASTQ format with mock quality scores
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 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
+
IIIIIIIIIIThe FASTA output contains the same read identifier and sequence, without the + separator or quality string:
>read_1 sample
ACGTRYSWKMFor multiple FASTQ records, each read becomes a separate FASTA record:
>read_1
ACGTACGT
>read_2
TTGGAACCThe 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.
| Input | Description |
|---|---|
Input | FASTQ text containing one or more sequencing reads. Accepts pasted text or file uploads. Common extensions: .fastq, .fq, .txt. Maximum file size: 100 MB. |
| Setting | Description |
|---|---|
Quality threshold | Filters reads by average quality score. No filtering keeps every valid read. Q10+, Q20+, and Q30+ keep only reads whose average quality meets or exceeds the selected threshold. |
Quality encoding | Selects how quality characters are converted into numeric scores. Use Phred+33 for Sanger and modern Illumina data, Phred+64 for older Illumina data, and Solexa+64 for early Solexa-format reads. |
Add average quality to headers | Appends the calculated average quality to each FASTA header. Leave disabled to preserve headers exactly. |
Trim low-quality ends | Removes bases below the trim threshold from both ends of each read before length filtering, quality filtering, and FASTA output. |
Trim threshold | Minimum per-base quality score to keep at read ends when trimming is enabled. |
Filter by read length | Keeps only reads whose post-trimming length falls between the selected minimum and maximum length. |
Minimum length | Shortest read length to keep when length filtering is enabled. |
Maximum length | Longest read length to keep when length filtering is enabled. |
Remove reads containing N | Excludes reads containing unknown N bases. Other IUPAC ambiguity symbols are still accepted. |
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.
| Output | Description |
|---|---|
| FASTA file | Converted FASTA records for reads that pass validation and selected filters. |
| Conversion summary | Counts input records, output records, filtered reads, trimmed reads, selected quality encoding, active settings, and warnings. |
| FASTA preview | Rendered FASTA text for quick inspection before copying or downloading. |
FASTQ records contain four logical sections:
@ and contains the read identifier plus optional description.A, C, G, T, U, R, Y, S, W, K, M, B, D, H, V, and N.+. It may be a bare + or repeat the read identifier.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.
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 is simple, but a few rules matter for downstream compatibility.
>, followed by the FASTQ header without the leading @.Add average quality to headers is enabled, the read's average quality is appended to the FASTA header.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.
| Input format | Best converter | Use when |
|---|---|---|
| FASTQ sequencing reads | FASTQ to FASTA | You need to remove quality-score lines from read data. |
| FASTA sequences needing FASTQ | FASTA to FASTQ | You need synthetic quality strings for FASTA records. |
| TXT or pasted sequence text | TXT to FASTA | You have raw DNA, RNA, or protein text without FASTQ quality lines. |
| CSV or spreadsheet-like text | CSV to FASTA | Sequence IDs and sequences are stored in columns. |
| GenBank records | GenBank to FASTA | You want sequence records from annotated GenBank files. |
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.
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.
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.
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.
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.