FASTA to CSV Converter for DNA and Oligo Sequences

Convert oligonucleotide sequences between FASTA, CSV, TSV, and plain text formats for vendor ordering (IDT, Twist Bioscience, GenScript), including CSV to FASTA / FASTA to TSV / TSV to FASTA workflows. Features automatic format detection, IUPAC nucleotide validation, reverse complement for primer design, deduplication, and batch processing. Process thousands of oligo pool sequences with browser-default conversion and explicit save controls.

Generic sequence conversion before vendor-specific export

Example input: FASTA records, CSV rows, TSV rows, or plain sequence lists that need cleanup.

Use this for: FASTA to CSV, CSV to FASTA, deduplication, reverse complement, uppercase, and IUPAC validation.

Before ordering: run Batch QC or open Vendor Format Adapter for order-file columns.

Input & Options

Common conversions

Dashboard Library

Use saved sequences as this tool's input.

Lines: 1 | Chars: 0

Processing Options

ID Modification (Optional)

Results

No results yet

Select format and convert your sequences

Common conversion tasks

FASTA to CSV, CSV to FASTA, and tab-delimited sequence examples

Each task uses the same browser-default parser as the calculator above, so examples here match the output columns and file formats produced by the tool.

FASTA to CSV

Convert FASTA records into spreadsheet rows with the default CSV columns ID,Sequence,Description.

Input FASTA

>pool_1 Forward primer
ATCGATCGATCG
>pool_2 Reverse primer
GCTAGCTAGCTA

Output CSV

ID,Sequence,Description
pool_1,ATCGATCGATCG,Forward primer
pool_2,GCTAGCTAGCTA,Reverse primer

CSV to FASTA

The parser auto-detects an ID column such as ID, Name, or Sequence Name, plus a sequence column such as Sequence, Oligo Sequence, Primer, or Probe.

Input CSV

Name,Sequence,Notes
oligo_A,ATCGATCGATCG,screening row
oligo_B,GCTAGCTAGCTA,control row

Output FASTA

>oligo_A screening row
ATCGATCGATCG
>oligo_B control row
GCTAGCTAGCTA

FASTA to TSV

Multi-line FASTA records are merged into a single-line sequence row, then written as tab-delimited text for tools that prefer TSV.

Input FASTA

>wrapped_1 Multi-line record
ATCGATCG
ATCGATCG
>wrapped_2 Multi-line record
GCTAGCTA
GCTAGCTA

Output TSV

ID	Sequence	Description
wrapped_1	ATCGATCGATCGATCG	Multi-line record
wrapped_2	GCTAGCTAGCTAGCTA	Multi-line record

Prepare FASTA Sequences for IDT, Twist, or GenScript CSV Orders

Convert FASTA into a clean CSV first, then map those rows into the exact vendor upload columns for scale, purification, plate position, and ordering notes.

Open Vendor Format Adapter

Validate IUPAC Codes, Remove Duplicates, and Clean Case

After format conversion, check ambiguity codes, duplicate rows, sequence length, and synthesis-risk flags before sending the table to an ordering workflow.

Run Batch Sequence QC

FASTA to CSV and Sequence Table Conversion

Bioinformatics sequence data often moves across multiple file formats. FASTA is the standard format for sequence databases and analysis tools, while CSV and TSV are used for spreadsheet review, vendor ordering, and data management. The Format Converter handles bidirectional conversion between these formats with automatic format detection.

FASTA format stores sequences with a header line (starting with ">") followed by the sequence on subsequent lines. CSV (comma-separated values) and TSV (tab-separated values) store sequences in tabular format with columns for name, sequence, and optional metadata. Converting between these formats manually is error-prone, especially with large datasets — our tool processes thousands of sequences instantly and validates each one.

Use this page for FASTA to CSV, CSV to FASTA, TSV cleanup, deduplication, reverse complement, uppercase, and IUPAC validation. It also covers FASTA to TSV and TSV to FASTA when you need tab-delimited sequence tables. When an order needs vendor-specific columns, open Vendor Format Adapter after the generic conversion is clean.

Use this page for CSV to FASTA, FASTA converter, and FASTA to CSV cleanup before vendor-specific export. CSV to FASTA / FASTA to TSV / TSV to FASTA workflows use the same parser and output controls, so the visible result format matches the file you download.

Additional features include reverse complement generation (essential for designing antisense primers), sequence deduplication (removing identical sequences that waste synthesis resources), and IUPAC code validation (catching invalid characters before vendor submission). Calculations run in your browser by default. Dashboard History can store the full input snapshot when auto-save, session, or account history is enabled; Library saves and membership/API workflows can send sequence assets by design.

How to Use the Format Converter

  1. Paste your sequences in the input field or upload a file (FASTA, CSV, or TSV). The converter auto-detects the input format.
  2. Select the desired output format: FASTA, CSV, or TSV.
  3. Enable optional processing: reverse complement, deduplication, uppercase conversion.
  4. Click "Convert" to process all sequences with automatic validation.
  5. Review any warnings (invalid characters, duplicate sequences) before downloading.
  6. Download the converted file or copy the output directly from the text area.

Frequently Asked Questions

How do I convert FASTA to CSV online?
Paste the FASTA records, choose the FASTA to CSV preset or set input to FASTA and output to CSV, then convert. The browser creates a spreadsheet-ready table by default; optional History, Library, membership, and API saves follow the shared data boundary.
Can it handle multi-line FASTA records?
Yes. Wrapped FASTA records are parsed as one sequence per header, so sequence lines below the same header are merged before CSV, TSV, FASTA, or text output is generated.
What CSV columns does the converter create?
CSV output creates ID,Sequence,Description by default. You can turn off the description column when you only need ID and Sequence for a compact table.
What is the difference between FASTA to CSV and FASTA to TSV?
FASTA to CSV uses commas between columns and works well for spreadsheet imports. FASTA to TSV uses tabs between columns, which is useful when sequence descriptions may contain commas or when a downstream tool expects tab-delimited text.
Can I convert CSV or TSV back to FASTA?
Yes. The converter reads CSV or TSV tables, detects ID and sequence columns, and writes each row back as a FASTA record with the description preserved when present.
What is FASTA format?
FASTA format is a text-based format for representing nucleotide or protein sequences. Each entry starts with a ">" symbol followed by a description line (header), and the sequence itself on subsequent lines. Example: >Primer_1\nATCGATCGATCG. The format was originally developed for the FASTA alignment tool and is now the most widely used sequence format in bioinformatics. Our converter handles both single-line and multi-line FASTA sequences.
How do I prepare sequences for IDT or Twist orders?
IDT requires sequences in plate-map format (CSV or Excel with specific column names: Name, Sequence, Scale, Purification). Twist Bioscience accepts CSV with Name and Sequence columns. Our Vendor Format Adapter tool generates vendor-specific formats directly. However, if you have sequences in FASTA format and need a quick CSV for vendor ordering, this Format Converter is the first step — convert to CSV, then use the Vendor Format Adapter for final formatting.
What are IUPAC ambiguity codes?
IUPAC codes extend the standard DNA alphabet (A, T, C, G) with ambiguity codes that represent multiple possible bases: R = A or G (purine), Y = C or T (pyrimidine), S = G or C (strong), W = A or T (weak), K = G or T, M = A or C, B = not A, D = not C, H = not G, V = not T, N = any base. Our converter validates against the full IUPAC alphabet and flags non-standard characters.
Can I convert multi-line FASTA to single-line?
Yes. Multi-line FASTA (where long sequences are wrapped at 60 or 80 characters per line) is common in genomic databases. Our converter automatically joins multi-line sequences into single-line format during conversion. When outputting FASTA, you can choose between single-line (compact) and multi-line (wrapped at 80 characters) format.
How does deduplication work?
Deduplication identifies and removes sequences that appear more than once in your dataset. Comparison is case-insensitive (ATCG = atcg = AtCg). When duplicates are found, the first occurrence is kept and subsequent copies are removed. The tool reports the number of duplicates found. This is particularly useful for oligo pools where duplicate sequences waste synthesis resources without adding experimental value.

Related Tools

Vendor Format Adapter

Generate vendor-specific order files for IDT, Twist, GenScript, and Dynegene.

Batch Sequence QC

After format conversion, validate all sequences for synthesis compatibility.

GC Content Analyzer

Analyze GC content for converted sequences to check synthesis suitability.

Review request

Check a result or ordering detail

Send the calculation, settings, or pool submission detail that needs a second look.

Related reading

Continue with the page or tool that matches the next decision in your experiment.

Pre-Order Oligo Pool QCBatch Sequence QCVendor Format AdapterFormat GuideSupported Vendors