GTO suite
57 opssequence · format · genomic · amino acid · info · text
Workflows
Build workflows
Drag tools into a workflow and test it in your browser on small data. Export it as one file, ready to run where your data lives.
How it works
From a quick test to a full run
- 01
Build
Drag tools onto the canvas and connect them. Each connection shows the file type it carries.
- 02
Test
Run it in your browser on a small sample. Results open next to the graph, and nothing is uploaded.
- 03
Run on the full data
Export the workflow as one JSON file, then share it or run it where the data is.
Where it can run ↓
See it in action
Watch a workflow run in the browser
Tutorials
Learn by doing
14 hands-on tutorials with small example data and the result you should get. Each one runs in your browser and ends with an exercise. New here? Start with “Map reads to a reference”.
Group by
One tool
One input, one tool: the simplest workflow.
A chain of tools
Each tool feeds the next.
- 20 min
Map reads to a reference
Align reads with minimap2, sort them with samtools and count how many mapped. Every move in the editor is shown.
minimap2 · samtools
- 25 min
Build a viral consensus genome
Call a sample’s consensus with ViralConsensus and check that it finds the mutations you know are there.
minimap2 · samtools · ViralConsensus
- 30 min
Amplicon sequencing of a virus
Trim primers, call variants and build a consensus with iVar, as in SARS-CoV-2 surveillance.
minimap2 · samtools · iVar
- 20 min
Assemble a small genome from reads
Put a phage genome back together without a reference, then check it against the known genome.
fermi-lite · minimap2
- 20 min
Align sequences and build a tree
Align eight sequences with muscle, infer their tree with FastTree and compare them with TN93.
muscle · FastTree · TN93
Branches
One input feeds several tools, so you compare results side by side.
- 15 min
First steps with DNA sequences
Count bases, cut a gene out of a genome and read it from the other strand.
seqtk
- 15 min
Check and clean reads
Filter low-quality reads with fastp and count what is left, before and after.
fastp · seqtk
- 20 min
Find where coverage drops
Measure how much of a genome is covered and list the regions where an amplicon failed.
minimap2 · samtools · gawk
- 15 min
Explore and filter variants
Summarise a VCF, keep the variants with enough quality and depth, and turn them into a table.
bcftools
Several inputs
Two or more files meet in one tool.
- 15 min
Clean and merge paired-end reads
Filter read pairs and merge the ones that overlap into single longer reads.
fastp · seqtk
- 15 min
Which genes do the variants fall in?
Overlap variants with gene coordinates and see why one variant can land in two genes.
bcftools · bedtools
- 15 min
Compare two related genomes
Align two phage genomes, measure how similar they are and see why a circle aligns in two pieces.
minimap2
Getting started and teaching
No prior knowledge needed; good for a class.
Sequencing labs and core facilities
Checking and preparing sequencing data.
- 15 min
Check and clean reads
Filter low-quality reads with fastp and count what is left, before and after.
fastp · seqtk
- 15 min
Clean and merge paired-end reads
Filter read pairs and merge the ones that overlap into single longer reads.
fastp · seqtk
- 20 min
Find where coverage drops
Measure how much of a genome is covered and list the regions where an amplicon failed.
minimap2 · samtools · gawk
Virology and public health
Viral genomes and genomic surveillance.
- 25 min
Build a viral consensus genome
Call a sample’s consensus with ViralConsensus and check that it finds the mutations you know are there.
minimap2 · samtools · ViralConsensus
- 30 min
Amplicon sequencing of a virus
Trim primers, call variants and build a consensus with iVar, as in SARS-CoV-2 surveillance.
minimap2 · samtools · iVar
Clinical and human genetics
Working with variants.
Microbiology and genomics research
Genes, assemblies and genome comparison.
- 15 min
Find the genes in a genome
Predict a phage’s genes with Prodigal, act on its error message and compare with the annotation.
Prodigal
- 20 min
Assemble a small genome from reads
Put a phage genome back together without a reference, then check it against the known genome.
fermi-lite · minimap2
- 15 min
Compare two related genomes
Align two phage genomes, measure how similar they are and see why a circle aligns in two pieces.
minimap2
Evolution and phylogenetics
How sequences and species are related.
Reads and quality
Raw sequencing reads.
Mapping and coverage
Reads placed on a reference.
- 20 min
Map reads to a reference
Align reads with minimap2, sort them with samtools and count how many mapped. Every move in the editor is shown.
minimap2 · samtools
- 20 min
Find where coverage drops
Measure how much of a genome is covered and list the regions where an amplicon failed.
minimap2 · samtools · gawk
Variants and consensus
Where a sample differs from the reference.
- 25 min
Build a viral consensus genome
Call a sample’s consensus with ViralConsensus and check that it finds the mutations you know are there.
minimap2 · samtools · ViralConsensus
- 30 min
Amplicon sequencing of a virus
Trim primers, call variants and build a consensus with iVar, as in SARS-CoV-2 surveillance.
minimap2 · samtools · iVar
- 15 min
Explore and filter variants
Summarise a VCF, keep the variants with enough quality and depth, and turn them into a table.
bcftools
- 15 min
Which genes do the variants fall in?
Overlap variants with gene coordinates and see why one variant can land in two genes.
bcftools · bedtools
Genomes and genes
Whole sequences, their genes and assemblies.
- 15 min
First steps with DNA sequences
Count bases, cut a gene out of a genome and read it from the other strand.
seqtk
- 15 min
Find the genes in a genome
Predict a phage’s genes with Prodigal, act on its error message and compare with the annotation.
Prodigal
- 20 min
Assemble a small genome from reads
Put a phage genome back together without a reference, then check it against the known genome.
fermi-lite · minimap2
- 15 min
Compare two related genomes
Align two phage genomes, measure how similar they are and see why a circle aligns in two pieces.
minimap2
Phylogenetics
Alignments and trees.
Teaching a class? Each tutorial includes its data and a finished workflow file, so students can import it and catch up at any step.
Catalogue
What you can chain together
The 34 signed recipes in the public BioChef catalogue, grouped by what they do. Every tool runs as WebAssembly in the browser; 15 also have a native build for the agent.
Alignment & mapping
6minimap2 · lastz · mummer4/nucmer · ssw · ksw2 · edlib
Variants & consensus
3bcftools · ivar · viralconsensus
BAM/SAM & QC
3samtools view/sort/stats · fastp · samblaster
MSA & phylogenetics
6muscle · kalign · abPOA · fasttree · ASTER · tn93
Genome intervals
2bedtools intersect · cgranges coverage
Assembly, ORFs & methylation
3fermi-lite assemble · prodigal · modbam2bed
Sequence toolkits
2seqtk · gffread — subseq · convert · filter
Text, JSON & shell
5gawk · grep · sed · jq · coreutils
Recently added
3trimal · wgsim · yak
Badges count recipes per family (GTO counts operations); 188 operations in all. New recipes are added by the community. 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
Two places to run
Live
In your browser
For building and testing. Tools run client-side as WebAssembly on small data, with nothing to install and nothing uploaded.
Emscripten · biowasm · signed digest from the registry
In development
Next to your data
For full runs. The BioChef agent runs the same signed tools on your workstation, a server or a secure environment, so large or sensitive data never has to move.