FASTA to CSV Converter

Turn a FASTA or multi-FASTA file into a spreadsheet-ready table — one row per record with id, description, sequence and length, plus optional GC content and base counts. Runs entirely in your browser, nothing is uploaded.

What this tool does

Paste a FASTA or multi-FASTA file and get a spreadsheet-ready table back — one row per record. By default each row carries the record's id, its description, the full sequence and its length; wrapped sequence lines are joined back into a single field first.

Nothing is uploaded. The parsing runs locally in your browser using WebAssembly, so it works offline and needs no sign-up.

Columns

Column	When	What it holds
`id`	always	The header text up to the first space (or the whole header, see below).
`description`	header handling = split	Whatever follows that first space.
`sequence`	Sequence column on	The record's sequence with all wrapped lines joined.
`length`	Length column on	Number of sequence characters — gaps and ambiguity codes such as `N` count.
`gc_percent`	GC content on	`(G+C) / (A+C+G+T) × 100`, two decimals, case-insensitive; `N` and gaps are excluded from both sides.
`a_count` … `other_count`	Base counts on	Case-insensitive counts of `A`, `C`, `G`, `T` and everything else.

Options

Option	What it does
Delimiter	`Comma` for `.csv`, `Tab` for `.tsv`, or `Semicolon`/`Pipe` when your spreadsheet uses a comma as its decimal separator.
Header handling	Split into id + description (default), Id only (drops the description column), or Whole header line as id (keeps `>gi\|123\|ref\|NM_000.1 Homo sapiens` intact in one cell).
Write a header row	On by default so the table opens with named columns. Turn it off for a bare data table.
Sequence / Length columns	Both on by default. Turn the sequence off for a names-and-metrics table.
GC content / Base counts	Add the extra metric columns described above.
Uppercase sequence	Normalises `acgt` → `ACGT` in the sequence column only.
Drop duplicate sequences	Keeps the first record of each identical sequence (compared case-insensitively).

Worked example

Input:

>seq1 first sequence
ACGTACGTNN
>seq2
acgt

Default output — comma delimiter, header row, id split from description:

id,description,sequence,length
seq1,first sequence,ACGTACGTNN,10
seq2,,acgt,4

seq2 has no description, so that cell is empty. Now switch GC content and Base counts on and the same input gives:

id,description,sequence,length,gc_percent,a_count,c_count,g_count,t_count,other_count
seq1,first sequence,ACGTACGTNN,10,50.00,2,2,2,2,2
seq2,,acgt,4,50.00,1,1,1,1,0

seq1 is 10 characters long, but its two Ns land in other_count and are left out of the GC calculation — 4 of its 8 unambiguous bases are G or C, so gc_percent is 50.00.

Limits and edge cases

The input must contain at least one > header line. Sequence data appearing before the first header is rejected with the offending line number.
Up to 50,000 records per conversion. Split a larger file and convert it in parts; very large inputs are also bounded by your device's memory.
Fields are quoted per RFC 4180: any value containing the delimiter, a double quote or a line break is wrapped in " and its inner quotes are doubled. Descriptions with commas are therefore safe in CSV mode.
Blank lines are ignored, CRLF line endings are normalised, and a header with no sequence after it yields an empty sequence cell with length 0.
length, gc_percent and the base counts are computed from the original sequence, so Uppercase sequence never changes them.

FAQ

How does the tool decide what is the id and what is the description?

With the default Split into id + description setting, everything up to the first whitespace character in the header becomes id and the remainder becomes description. >seq1 first sequence therefore yields seq1 and first sequence. If your identifiers contain spaces you care about, choose Whole header line as id to keep the header in a single cell.

Can I get a TSV instead of a CSV?

Yes — set Delimiter to Tab. The columns and options are identical; only the separator changes, and commas inside descriptions no longer need quoting. Save the result with a .tsv extension.

What does the length column count?

Every character of the joined sequence, including ambiguity codes like N and alignment gaps like -. That matches how most FASTA tooling reports length. If you need the unambiguous base total instead, switch on Base counts and add a_count + c_count + g_count + t_count.

Does it work with protein FASTA, not just DNA?

Yes. Parsing, the id/description split, length and the CSV quoting are all sequence-agnostic. The gc_percent column is only meaningful for nucleotide sequences, and for protein input the base counts put nearly every residue into other_count, so leave those two options off.

Is my sequence data uploaded anywhere?

No. The conversion runs entirely in your browser using WebAssembly. Your sequences 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 fasta-to-csv ">seq1 first sequence
ACGTACGTNN
>seq2
acgt"

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/fasta-to-csv/?fasta=%3Eseq1%20first%20sequence%0AACGTACGTNN%0A%3Eseq2%0Aacgt&delimiter=comma&header_mode=split&header_row=true&include_sequence=true&include_length=true&include_gc=true&include_base_counts=true&uppercase=true&dedupe=true

Machine-readable descriptor: tool.json — title + parameters JSON Schema for agents.