Sequence File Converter and Analyzer

FASTA · FASTQ · FASTQ.gz · AB1 (Sanger trace) · GenBank · CSV/TSV · raw text — core written in Rust, compiled to WebAssembly, runs 100% offline in your browser.

rust core → wasm · no python, no server

1 · Load sequences drag & drop, browse, paste, or demo

Drop a sequencing file here, or click to browse
Accepted: .fa .fasta .fas .fna .fastq .fq .fastq.gz .fq.gz .fa.gz .fasta.gz .txt .seq .csv .tsv .gb .gbk .genbank .ab1 .abl .fsa
No file handy? Load a demo:

2 · File summary

Load a sequence file above to see its summary (records, bases, GC%, ambiguous N, quality).
#ID / descriptionLengthGC%ATGCNQualityPreview

3 · Convert & export generate FASTA, FASTQ, or FASTQ.gz

Phred+33 constant value (Q40 ≈ "I"). Only used for sequence-only inputs.
Output reverse-complemented strands
Standard genetic code; * = stop, X = ambiguous codon.
Output preview (first 60,000 characters)

About the Sequence File Converter and Analyzer

This tool converts between the sequence file formats you actually receive from sequencing providers and the ones you need to analyse, then reports the basic statistics worth knowing before you go further. It reads FASTA, FASTQ, gzipped FASTQ, AB1 Sanger trace files, GenBank and delimited CSV or TSV, and writes FASTA or FASTQ out.

The AB1 support is the part that saves the most time. Trace files arrive as binary AB1 from nearly every Sanger sequencing service, and ordinary text tools cannot read them. Parsing the base calls, the quality values and the chromatogram data directly removes the most tedious step in checking a Sanger result.

The engine is written in Rust and compiled to WebAssembly, so it is fast enough to handle real files, and it runs locally. Nothing is uploaded, which is what makes it usable on patient samples, embargoed constructs and unpublished sequences.

What this tool does

AB1 Sanger trace parsing

Read binary trace files from sequencing providers and extract base calls with their quality scores, so a Sanger result can be checked without converting it by hand.

Multi-format conversion

Convert between FASTA, FASTQ and delimited CSV or TSV in either direction, adapting output rather than forcing you to hand-edit.

gzip support

Handle .fastq.gz directly, decompressing in the browser and re-compressing on output if you ask for it.

GenBank import

Read GenBank records to pull out the sequence alongside its annotation, which is the common route for constructs ordered from a repository.

Quality and composition analysis

Report GC content, quality score distributions and counts of ambiguous bases so you can judge whether a file is fit for the analysis you have planned.

Frequently asked questions

Are my sequence files uploaded anywhere?

No. The Rust engine is compiled to WebAssembly and runs in your browser. Files are read into browser memory and processed on your own device, so clinical and unpublished sequences stay private.

What exactly does the AB1 conversion do?

It reads the binary trace file, decodes the chromatogram data and the base calls with their per-base quality scores, and writes the result as FASTA or FASTQ that any downstream tool can accept.

What counts as an ambiguous base?

Letters other than A, C, G and T or U, principally N for unknown plus the IUPAC ambiguity codes such as R, Y, S, W, K and M. A high count usually means low-quality bases, a mixed sample, or over-aggressive base calling.

Does converting to FASTA lose my quality scores?

Yes, because the FASTA format has nowhere to store per-base quality. Convert to FASTQ if the downstream tool needs quality values, for example when you intend to run quality control or trimming.

How large a file can it handle?

Files are loaded into browser memory, so practical limits depend on your device. Multi-gigabyte FASTQ files are better handled with a local install of the standard tools; this page suits the files that arrive from ordering a primer or a small construct.

Can I use the output directly with the other tools here?

Yes. The output is standard FASTA or FASTQ, so it can be loaded straight into the FASTA and FASTQ tools, the sequence aligner, or the FASTQ quality control page.

Related tools

All toolsFASTA/FASTQ ToolsText to FASTA ConverterSequencing Verification ReportNCBI FASTA AnalyzerFASTQ Quality Control

All processing happens locally in your browser. Nothing you upload is transmitted or stored, as described in the privacy policy.

Sequence File Converter and Analyzer | Ashif Raza