Assemble reads in your browser

Have sequencing reads rather than an assembled genome? Assemble them here first. The assemblers (Flye 2.9.6 for long reads, SPAdes 4.2 for Illumina reads, compiled to WebAssembly) run entirely on your own computer: your reads are never uploaded. Only the contigs you choose to annotate are sent to the server.

Reads

FASTQ or FASTA, optionally gzipped (.fastq.gz). The files are read directly from your disk; nothing is uploaded. Select several files of long reads to assemble them together.

Read type

Expected genome size (optional)

Only needed for the subsampling option below. Use k or m suffixes (100k, 0.2m).

Use the longest 50× of reads for the initial assembly (much faster for high-coverage phage data; needs a genome size)

Uneven coverage mode (Flye --meta) (for mixed samples, e.g. a phage with host contamination; disables subsampling)

Threads

CPU cores to use on your computer.

Assembled contigs

Tick the contigs to annotate. The longest well-covered contigs are pre-selected; phages are usually the highest-coverage contigs, often circular. Up to 20 contigs and 2,000,000 bp per job.

Annotate	Contig	Length (bp)	Coverage	Circular	Repeat

Annotate the selected contigs

The selected contigs are submitted as one job, exactly like a FASTA uploaded on the submit page, with the same options.

Gene predictor

Fast mode (recommended -- skips slower pharokka steps)

Email (optional)

Only used to send you your results link. No account, no mailing list.

Advanced options (pharokka / phold / phynteny parameters)

Every real CLI flag is shown next to its label, with the tool's own default. Leave a field as-is to use that default. Values are re-validated on the server regardless of what's shown here.

Metagenome mode

Metagenome mode -m/--meta

Auto turns metagenome mode on when your upload has 2 or more contigs (as recommended by pharokka), and off for a single contig. pharokka itself refuses --meta with only 1 contig, so "Always on" is automatically skipped in that case -- we'll tell you what was actually used on the job status page.

Pharokka

Coding table -c/--coding_table

E-value threshold -e/--evalue

Default 1e-05. Allowed range 1e-30–0.1.

MMseqs2 sensitivity --sensitivity

Default 8.5. Allowed range 1.0–10.0.

Reorient genome to terminase large subunit --dnaapler

Skip INPHARED closest-relative search --skip_mash

Skip tRNA / CRISPR / tmRNA annotation --skip_extra_annotations

Phold

E-value threshold -e/--evalue

Default 0.001. Allowed range 1e-30–0.1.

Foldseek sensitivity -s/--sensitivity

Default 9.5. Allowed range 1.0–10.0.

One GenBank file per contig --separate

Phynteny

Confidence threshold --confidence-threshold

Default 0.8 (0.0–1.0). Predictions below this confidence are reported but not treated as high-confidence calls.

By submitting you agree to the terms of use and accept that the selected sequences will be processed on shared infrastructure.