Node Categories
BioNodulo ships with 1,370 built-in operations across 61 categories, organized to follow the typical shape of a bioinformatics workflow: load data, QC it, process it, analyze it, and export results. This count comes from the app’s builtin node catalog; several operations may use the same upstream tool. Categories with a dedicated page are linked. The table groups related catalog categories for a quick overview.
| Category | Example nodes | Description |
|---|---|---|
| Input / Output | FASTQ, FASTA, VCF, GFF, File, Directory, Sample Sheet | Data loading |
| Quality Control | FastQC, MultiQC, QualiMap | Sequence quality assessment |
| Read Preprocessing | fastp, Trimmomatic, Cutadapt | Adapter trimming and filtering |
| Alignment | BWA, Bowtie2, Minimap2, STAR, HISAT2 | Read alignment, including index builders |
| SAM/BAM Processing | samtools sort/index/flagstat/view/merge/stats | Alignment processing |
| SeqKit and EMBOSS operations | SeqKit, EMBOSS | Sequence filtering, transformation, and analysis |
| CSVtk and VCF-lib operations | CSVtk, VCF-lib | Table processing and variant-file operations |
| TaxonKit operations | TaxonKit | Taxonomy lookup and conversion |
| Variant Calling | GATK, bcftools, FreeBayes, VCFtools | SNP/indel detection |
| Assembly | SPAdes, MEGAHIT, Flye, Canu, Unicycler, QUAST | Genome assembly |
| Annotation | Prokka, Bakta, eggNOG | Genome annotation |
| Phylogenetics | MAFFT, ClustalΩ, IQ-TREE, FastTree, RAxML | Tree construction |
| RNA-Seq | Salmon, Kallisto, featureCounts, StringTie | Expression analysis |
| Metagenomics | Kraken2, Bracken, MetaPhlAn, HUMAnN, MaxBin, CheckM | Microbial profiling |
| ChIP-Seq | MACS2, BEDTools, deepTools | Peak calling and coverage |
| Single Cell | Cell Ranger | scRNA-seq analysis |
| Spatial Transcriptomics | Space Ranger, Squidpy, Scanpy, Seurat, Cell2location, Baysor | Visium QC, spatial clustering, UMAP visualization, deconvolution, segmentation |
| Long Read | Dorado, Chopper, NanoPlot, Modkit | ONT basecalling, demux, QC, modified bases |
| Proteomics | Sage, Percolator, FragPipe, MSFragger, MaxQuant, DIA-NN, OpenMS | MS search and FDR |
| Protein Structure | UniProt, AlphaFold DB, RCSB PDB | Sequence lookup, predicted/experimental structures |
| Metabolomics | XCMS, CAMERA, SIRIUS, MZmine, MetaboAnalystR, MS-DIAL | LC-MS peaks, annotation, statistics |
| Epigenomics | Bismark, MethylDackel, DSS, Modkit, deepTools, Hi-C tooling | WGBS methylation, DMR, chromatin contacts |
| CRISPR | Guide RNA Design, Cas-OFFinder, CRISPResso2, MAGeCK | Guide design, off-targets, screens |
| Pangenomics | PGGB, Minigraph, Minigraph-Cactus, ODGI, vg | Graph construction, QC, visualization |
| Synthetic Biology | SBOL, COPASI, iBioSim, Cello | BioCAD import, circuit compilation, simulation |
| HPC | Job Submit, Status Check | Cluster job submission |
| BioPython | SeqIO, BLAST, MSA, Sequence Stats | Python bioinformatics tools |
| R Integration | R Script, R Plot, DataFrame Builder | R statistical computing |
| AI & LLM | Literature Search, Pipeline Advisor, Report Generator, Sequence Analysis | AI-assisted analysis nodes |
| ML Design | Candidate Generator, Group Relative Optimizer, Validation Metrics | mRNA/design optimization campaigns |
| Flow Control | Loop, Subgraph, Branch, Collect | Workflow structure and iteration |
| Utility | Generic Command, View Text, Collect Files, Merge VCF, Note, Reroute | Helpers |
Tool Atlas
In the editor, open Nodes → Open Tool Atlas to search the current builtin catalog by name, alias, description, format, or supplied ontology term. Choose an operation to inspect Data flow candidates (matching declared port types) or Related tools (shared metadata and documented relationships). Select a connection to see its reason and any recorded source. Add to workflow places the selected operation on the canvas; it does not connect or run it.
The 1,370 operations are the bundled builtin node definitions, not a complete index of bio.tools or a claim that every tool runs in every environment. Some nodes need external software or credentials. A matching port type suggests a possible connection, not verified scientific or runtime compatibility.
See also
- Custom Nodes Guide, build your own nodes
- Nodes and Connections, how nodes fit together in a graph