FASTQ to FASTA converter

How to convert FASTQ to FASTA?

Paste FASTQ reads or upload a .fastq, .fq, or .txt file, then select Convert to get a FASTA file. ProteinIQ validates each record and removes its quality string. Sequence case and header descriptions are preserved; duplicate read identifiers receive numeric suffixes with a warning. Optional filters can remove low-quality reads or trim their ends.

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 retained read becomes a separate FASTA record. This input:

@read_1
ACGTACGT
+
IIIIIIII
@read_2
TTGGAACC
+
HHHHHHHH

produces:

>read_1
ACGTACGT
>read_2
TTGGAACC

With Trim low-quality ends enabled and the default Q15 trim threshold, this read:

@trimmed_read
TTACGTACGTAA
+
#,,,IIIIII,,

becomes:

>trimmed_read
GTACGT

Four bases are removed from the start and two from the end. The warning and summary report one trimmed read. If trimming removes every base, that read is discarded rather than written as an empty FASTA record.

Input

Wrapped sequence and quality sections are supported. Their joined lengths must match. Quality lines beginning with @ or + remain quality data until the expected number of characters has been read.

Settings

Results

Results open on the FASTA preview, with a line showing how many reads were converted. Downloads contains the FASTA file, conversion summary, and run.log; the log also appears in the shared Logs tab. Uploaded filenames supply the FASTA basename, such as reads.fq becoming reads.fasta.

How FASTQ to FASTA conversion works

FASTQ records contain four logical sections:

• Header: Starts with @, immediately followed by a nonempty read identifier and optional description.
• Sequence: 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. Letter case and the supported gap markers . and - are preserved.
• Separator: Starts with +. It may be a bare + or repeat the read identifier, with an optional description. A different identifier is rejected.
• 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 fail the entire conversion. Check the record number in the error, correct its header, separator, sequence, or quality section, and try again. Quality characters must be printable ASCII and valid for the chosen encoding. Decimal quality values, color-space reads, compressed data, and text extracted from Word or PDF files are outside this tool's input format.

These format and encoding rules follow the FASTQ format paper by Cock and colleagues and Biopython's quality-format reference.

FASTQ to FASTA filtering rules

Filtering and trimming are optional. With the default settings, every valid read is converted.

Quality filtering uses the arithmetic mean of Phred scores after optional end trimming. For example, scores Q0 and Q40 average to Q20. This does not mean the two bases have 99% average accuracy. The summary's average output quality is the unweighted mean of the retained reads' average scores, rather than a pooled mean across all bases.

The selected encoding matters because an ASCII character can represent different scores in Phred+33, Phred+64, and Solexa+64 files. Encoding is selected explicitly; overlapping character ranges prevent reliable automatic detection. Check the data provider's format if the encoding is uncertain.

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 checks the sequence remaining after trimming. A read whose only N bases were trimmed away can pass. Other IUPAC ambiguity symbols such as R, Y, S, and W remain valid. Fully trimmed reads are always discarded; if no reads remain, lower the thresholds or disable filters.

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 @. Duplicate identifiers receive _2, _3, or the next unused numeric suffix before the description, and the change is reported. For example, two headers named read sample A and read sample B become read sample A and read_2 sample B.
• 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 Illumina 1.3 to 1.7 files and Solexa+64 for early Solexa-format reads. Confirm the source encoding before using quality-based filters; a file can be valid under more than one encoding.

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.