FASTQ to FASTA converter

Convert FASTQ sequencing reads to FASTA while preserving headers and sequence case by default.

Input

FASTQ input

Quality threshold

Quality encoding

Add average quality to headers

Trim low-quality ends

Trim threshold

Filter by read length

Minimum length

Maximum length

Remove reads containing N

Output

Configure inputs to begin

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

How to convert FASTQ to FASTA?

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:

Text

@read_1 sample
ACGTRYSWKM
+
IIIIIIIIII

The FASTA output contains the same read identifier and sequence, without the + separator or quality string:

Text

>read_1 sample
ACGTRYSWKM

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

Text

>read_1
ACGTACGT
>read_2
TTGGAACC

The 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.

Results

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.

How FASTQ to FASTA conversion works

FASTQ records contain four logical sections:

Header: Starts with @ and contains the read identifier plus optional description.
Sequence: Contains nucleotide letters. ProteinIQ 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.
Separator: Starts with +. It may be a bare + or repeat the read identifier.
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 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.

FASTQ to FASTA filtering rules

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 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 @.
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.

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.

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 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.

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.

Related tools

FASTA to FASTQ Converter

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GenBank to FASTA Converter

Convert GenBank files to FASTA format

TXT to FASTA converter

Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads

DNA to RNA converter

Convert DNA sequences to RNA (transcription) - replaces T with U

RNA to DNA converter

Convert RNA sequences to DNA (reverse transcription) - replaces U with T

GenBank Feature Extractor

Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features

Reverse complement generator

Generate reverse, complement, or reverse-complement of DNA/RNA sequences

DNA to Protein Converter

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Protein to DNA converter

Reverse translate protein sequences to possible DNA sequences

How to convert FASTQ to FASTA?

For one FASTQ record:

Text

@read_1 sample
ACGTRYSWKM
+
IIIIIIIIII

The FASTA output contains the same read identifier and sequence, without the + separator or quality string:

Text

>read_1 sample
ACGTRYSWKM

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

Text

>read_1
ACGTACGT
>read_2
TTGGAACC

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.

Results

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.

How FASTQ to FASTA conversion works

FASTQ records contain four logical sections:

Header: Starts with @ and contains the read identifier plus optional description.
Sequence: Contains nucleotide letters. ProteinIQ 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.
Separator: Starts with +. It may be a bare + or repeat the read identifier.
Quality: Contains one ASCII quality character per sequence letter.

FASTQ to FASTA filtering rules

Filtering is optional. With the default No filtering setting, every valid read is converted.

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 @.
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.

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.

FAQ

How do I convert a FASTQ file to FASTA format?

Does FASTQ to FASTA keep quality scores?

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?

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.