FASTQ to FASTA Converter
Strip the per-base quality lines from FASTQ reads and get clean FASTA — with optional length, mean-quality, wrap, rename and N-read filters. Runs entirely in your browser, nothing is uploaded.
What this tool does
Convert FASTQ sequencing reads to FASTA instantly, right in your browser.
Each FASTQ read is four lines — a header, the sequence, a + separator, and the
per-base quality string. This tool drops the + and quality lines, rewrites the
@ header as >, and (optionally) filters or reformats the reads. Nothing is
uploaded: it runs locally, works offline, and needs no sign-up.
Paste one or more reads, tune the options, and copy the FASTA out.
FASTQ vs FASTA
| Format | Lines per record | Carries quality? |
|---|---|---|
| FASTQ | 4 — @id, sequence, +, quality | Yes (per-base Phred) |
| FASTA | 2 — >id, sequence | No |
Options
| Option | What it does |
|---|---|
| Min read length | Drop reads shorter than N bases. 0 = keep all. |
| Min mean quality | Drop reads whose mean Phred quality is below the threshold. 0 = no quality filter. |
| Quality offset | How to decode quality characters: Phred+33 (Sanger / Illumina 1.8+, the modern default) or Phred+64 (old Illumina 1.3–1.5). Only matters when a quality filter is active. |
| Wrap width | Split each output sequence into fixed-width lines (e.g. 60 or 70). 0 = one line per sequence. |
| Rename headers | Replace every header with a sequential number (>1, >2, …). |
| Discard reads with N | Drop any read whose sequence contains an ambiguous N base. |
| Uppercase | Uppercase the sequence bases (acgt → ACGT). |
Worked example
Input (two reads):
@read1 sample
ACGTACGTNN
+
IIIIIIII##
@read2
ACGT
+
!!!!
Default conversion (no filters) → the quality lines are gone and @ becomes >:
>read1 sample
ACGTACGTNN
>read2
ACGT
Now set Min mean quality to 20 (offset Phred+33). The ! character is
Phred 0, so read2 (mean 0) is dropped, while read1 (mean ≈ 26) survives:
>read1 sample
ACGTACGTNN
Limits and edge cases
- Input must be well-formed FASTQ: a multiple of 4 lines, each header starting
with
@, each third line starting with+, and the quality string the same length as its sequence. A mismatch reports which read failed and why. - The quality filter needs the right quality offset — a quality character below the offset (a negative Phred) is reported as a likely wrong-offset error.
- Wrap width is capped at 1000 characters per line.
- Everything runs in the browser tab, so extremely large files are bounded by your device's memory; split very large FASTQ files before pasting.
FAQ
What is the difference between FASTQ and FASTA?
FASTQ stores four lines per read — a header, the sequence, a + separator, and a
per-base quality string — while FASTA stores just a header and the sequence. This
tool removes the quality information and keeps the sequence, converting @ headers
into > headers.
Which quality offset should I pick?
Use Phred+33 for anything modern (Sanger and Illumina 1.8 or newer) — this is the default. Use Phred+64 only for legacy Illumina 1.3–1.5 data. The offset only affects the mean-quality filter; if you leave that filter off, the setting is ignored.
How is the mean quality calculated?
Each quality character is decoded to a Phred score as ord(char) - offset, and the
scores are averaged across the read. A read is dropped when that average is below
your Min mean quality threshold. ! decodes to 0 (offset 33), I to 40.
Does the tool discard reads containing N?
Not by default — N-containing reads are kept so the conversion is loss-free. Turn
on Discard reads with N to drop any read whose sequence contains an ambiguous
N (or n) base.
Is my data uploaded anywhere?
No. The conversion runs entirely in your browser using WebAssembly. Your reads never leave your device, and the page keeps working offline once it has loaded.
Developer & Automation Access
Run it from the terminal
Same engine as this page, headless — via the gizza CLI:
gizza tool fastq-to-fasta "@read1 sample
ACGTACGTNN
+
IIIIIIII##"New to the CLI? Get gizza →
Open it by URL
Pre-fill and auto-run this tool with query parameters — the names match the API/CLI:
https://gizza.ai/tools/fastq-to-fasta/?fastq=%40read1%20sample%0AACGTACGTNN%0A%2B%0AIIIIIIII%23%23&min_length=0&min_quality=0&quality_offset=33&wrap=0&rename=true&strip_n=true&uppercase=trueMachine-readable descriptor: tool.json — title + parameters JSON Schema for agents.