FASTA to FASTQ Converter

How to convert FASTA to FASTQ?

To convert FASTA to FASTQ, paste records or upload a FASTA file, choose a synthetic quality score profile, and click Convert. The output preserves identifiers and record order, writes sequences in uppercase, and adds one Phred+33 quality character per position. Preview the result, then copy it or download the .fastq file.

For one FASTA record:

>read_1 sample
ACGTNACGTN

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

@read_1 sample
ACGTNACGTN
+
IIIIIIIIII

For multiple FASTA records, each sequence becomes a separate FASTQ record. With the default Q40 profile, this input:

>read_1
ACGTACGT
>read_2
TTGGAACC

produces:

@read_1
ACGTACGT
+
IIIIIIII
@read_2
TTGGAACC
+
IIIIIIII

FASTA does not store base-call confidence, so generated scores are synthetic. They are useful for examples and pipeline tests but cannot replace measured sequencing quality. Keep the original FASTQ when real scores matter. Assigning Q40 does not establish that a sequence is accurate.

Input

Wrapped sequence lines, spaces, tabs, non-breaking spaces, and invisible document formatting are removed before conversion. Full lines beginning with # are ignored as comments. Headers keep their descriptions; duplicate identifiers stay in source order.

Text before the first header and empty identifiers cause an error. Empty records and records with digits or invalid punctuation are skipped with warnings and included in the skipped count. Digits are never removed to rescue a record. If every record is invalid, conversion fails and explains what to correct.

Settings

Results

Preview opens first with a line showing converted records, total length, skipped records, and synthetic encoding. Files contains the FASTQ, conversion summary, and run.log; Logs shows the same downloadable log. Uploaded files retain their basename, for example reads.fa becomes reads.fastq and reads-summary.txt. Pasted input uses converted.fastq and converted-summary.txt.

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 header description, joins sequence lines, validates the sequence, and generates a quality string with the selected profile. Empty and invalid records are omitted with visible warnings. A sequence written on the header line, such as >read ACGT, is a header description, not an inline sequence.

The converter uses Phred+33 encoding: each numeric score becomes an ASCII character with code Q + 33. This follows the Sanger FASTQ convention described by Cock and colleagues. The NCBI SRA format guide also requires sequence and quality strings to have equal lengths. The probabilities below describe Phred scores, not measured confidence in these synthetic records.

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.

For Declining quality (Q40 to Q10), the input >read_1 followed by ACGT produces scores Q40, Q30, Q20, and Q10:

@read_1
ACGT
+
I?5+

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: Empty and 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.

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, within the tool's input limits. Each valid FASTA record becomes one FASTQ record. Empty and invalid records count as skipped in the summary and produce warnings.

Why was a FASTA record skipped?

The record had no sequence lines or contained an invalid character, such as a digit or an inline comment. Put sequence letters on lines below the header and put # comments on their own lines. Numbered database exports need cleanup before conversion; no bases are inferred from the numbers.

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.