Workflows

Build workflows

Drag bioinformatics tools into a DAG inside your browser tab. Outputs flow live, parameters re-execute on the fly, and the whole thing is just a static page that runs WebAssembly.

Editor preview

Drag, drop, and watch outputs flow

A four-node sketch of what the Workflow page looks like in the BioChef app. Click a node to see what feeds it and what it produces.

Workflow builder
WASMUI
UIInput FASTQWASMgto.fastq.infoWASMgto.fastq.to.fastaWASMgto.fasta.reverseUIOutput
Click nodes to explore connections

In practice

Example scenarios

Three things people actually do with the Workflow page today.

Triage

Sequencing data triage

Run fastp for QC and adapter trimming, then chain samtools view/stats/flagstat or GTO statistics to triage FASTQ or BAM/CRAM in seconds, no upload needed.

Data prep

Format conversion pipeline

Convert between FASTA, FASTQ, SEQ, BAM ↔ SAM (samtools), GTF ↔ GFF (gffread); reverse, complement, slice. All in one signed recipe.

Education

Teaching demo

Share a recipe link with a class. Anyone can open it in the browser and walk through the same DAG step by step.

Catalogue

What you can chain together

A snapshot of the tool families currently available in the BioChef catalogue. Every tool runs as WebAssembly in your browser tab.

GTO suite

57+

sequence · format · genomic · amino acid · info · text

seqtk

20+

FASTA/FASTQ — subseq · sample · trim · convert · stats

samtools

15+

BAM/SAM/CRAM — view · sort · index · mpileup · flagstat · stats

gffread

4+

GFF/GTF — convert · extract · filter · validate

MSA & phylogenetics

5+

muscle align · fasttree phylogenetic tree

fastp

3+

FASTQ QC · adapter trim · per-base report

Text & JSON utilities

4+

gawk · grep · jq — filter · pattern match · JSON query

And growing

+

New recipes added by the community

Counts approximate. Workflows can pipe FASTA, FASTQ, BAM, SAM, CRAM, VCF, BCF, BED, GFF, JSON, LIST and more between tools. See the full catalogue in the app →

Runtime

One runtime today

Every step runs in the browser via WebAssembly. Server-side runtimes are on the roadmap.

Live runtime

Browser WebAssembly

Every shipped tool runs entirely in your browser tab. No upload, no install, no server.

Where

Your browser tab

Compiled with

Emscripten · biowasm

Loaded by

Signed digest from registry