FASTA/FASTQ Tools
Process sequences with seqtk
About the FASTA/FASTQ Tools page
This page runs seqtk 1.3 compiled to WebAssembly, so you can do everyday sequence housekeeping in the browser: check base composition, take a random subset, convert between FASTA and FASTQ, or produce a reverse complement. Nothing is uploaded, and there is nothing to install.
seqtk is the Swiss-army knife for FASTA and FASTQ. It is fast, its output is stable, and it is a dependency in a huge number of published pipelines, so results here match what you would get locally.
Use it for quick checks on a reference, for preparing a manageable subset of a large assembly while developing a script, or for converting formats at the start of an exploratory analysis.
What this tool does
Base composition
seqtk comp reports the number and fraction of each base plus GC content per sequence, which is the quickest way to spot contamination, low-complexity regions or a truncated reference.
Subsampling
Draw a random fraction of sequences or reads, useful for building a small test dataset while developing a pipeline before running it on the full file.
Format conversion
Convert FASTQ to FASTA with quality values dropped, or FASTA back to FASTQ with uniform quality, for tools that only accept one of the two formats.
Reverse complement
Produce the reverse complement of every sequence, needed for building primer and construct files, inverted repeat checks and strand-specific workflows.
Example commands
seqtk compReport per-sequence base counts and GC fraction. The fastest check that a reference is what you think it is.
seqtk seq -rEmit the reverse complement of every sequence in the file.
seqtk sample -p 0.1Randomly keep 10 percent of sequences, giving a representative subset for quick iteration.
seqtk seq -AConvert FASTQ input to FASTA output, discarding the quality string.
Frequently asked questions
Do I need to install seqtk?
No. The tool is a WebAssembly build running inside your browser tab, so there is no installation, no dependency management and no waiting for a native binary to compile.
Is my sequence file uploaded to a server?
No. The file is read into browser memory and processed locally. Genomes, plasmids and any confidential sequence can be processed without transfer.
Does seqtk comp handle gzip-compressed input?
Yes. The file picker accepts .gz, so a bgzipped or gzip-compressed FASTA or FASTQ can be used directly.
What is a normal GC content for genomic DNA?
Roughly 40 to 60 percent for most eukaryotes, with microbial and organellar genomes sometimes outside that range. A strong deviation usually means contamination, a different organism, or a sequencing artefact rather than biology.
When should I use the sampler instead of head?
Use a random subsample for anything where order matters, such as estimating composition or splitting a training and test set. Taking the first N sequences is biased whenever the file is not already shuffled.
Can seqtk handle very large assemblies?
Because the file is loaded into browser memory, there is a practical size limit tied to your device. For multi-gigabyte assemblies, run seqtk locally instead.
Related tools
All processing happens locally in your browser. Nothing you upload is transmitted or stored, as described in the privacy policy.