Tools

Liatir ships with three built-in analysis surfaces: WASM plugins that run inside the app, native tools that delegate to binaries installed on your machine, and AI Tools that use local AI Models.

All of them share the same UI pattern, run history, and output model. They are interchangeable from the pipeline's perspective when their input and output types match.

WASM plugins

Compiled to WebAssembly and bundled with Liatir. Zero installation required. These tools work identically on every machine.

Tool	Description
FastQC	Per-base quality, GC content, adapter detection, duplication levels
seqkit stats	FASTA/FASTQ sequence counts, GC, length, N50

Native tools

Require the corresponding binary to be in your system PATH. Liatir checks availability when you open the tool page and surfaces install instructions (Homebrew, apt, conda) if the binary is missing.

Tool	Binary	Subcommand	Input formats
Samtools	samtools	flagstat	BAM, SAM, CRAM
Samtools faidx	samtools	faidx	FASTA, FASTA.GZ
BWA-MEM	bwa	mem	FASTA + FASTQ
Minimap2	minimap2	—	FASTA/MMI + FASTQ/FASTA
BCFtools	bcftools	stats	VCF, VCF.GZ, BCF, BCF.GZ
BCFtools filter	bcftools	filter	VCF, VCF.GZ, BCF, BCF.GZ
SnpEff	java + SnpEff JAR	—	VCF, VCF.GZ
fastp	fastp	—	FASTQ (single or paired-end)

AI Tools

AI Tools are documented separately because interpreting their results requires model-specific context.

AI Tool	Description
CellTypist Annotation	Single-cell cell-type labels from .h5ad inputs
Sequence Embedding	DNA/RNA/protein sequence embeddings
Genomic Variant Effect	Embedding-delta scores for variants
Regulatory Prediction	Predicted regulatory signal tracks
Protein Structure Prediction	Protein 3D structure prediction

Start with Local AI for bioinformatics if you are new to these outputs.

Scientific viewers

Viewers inspect output artifacts produced by tools and pipelines.

Viewer	Description
3D Structure Viewer	PDB/mmCIF/CIF structure inspection
Genome Track Viewer	BED and genome-track inspection
Single-cell Viewer	single-cell labels and preview artifacts

Common UI pattern

Every tool page follows the same layout:

1. Dependency check — if a native binary is missing, Liatir shows installation instructions.
2. Input form — file pickers pre-filtered by compatible extension, plus any tool-specific options.
3. Run button — starts the analysis and streams progress or logs when available.
4. Results panel — shows parsed stats, tables, text output, charts, and generated files.
5. Run history sidebar — all past runs for this tool, selectable to re-display their results.

Result views

Tool results are displayed in a consistent format:

• stats appear as readable key-value grids;
• long text output can be expanded when needed;
• charts are interactive where available;
• generated files appear above the report with actions.

Output files

Some tools produce output files as part of their results. These appear in the results panel above the stats sections, with two actions:

• Add to Data — registers the file in the Data library immediately, making it available as an input to the next step.
• Save as… — opens the system save dialog so you can copy the file to a location of your choice.

Run history

Each tool keeps a persistent run history. Selecting a past run in the sidebar re-renders its output without re-running the tool. Run records include:

• Tool name and version
• Input file paths
• Parsed results
• Output file references
• Timestamp

Pipeline integration

Tools expose compatible inputs and outputs to the pipeline builder. This allows an output file from one step to be connected to a compatible input in the next step. See Pipeline Overview for details.