Node Categories
BioNodulo ships with 975+ built-in nodes across 50+ categories, organized to follow the typical shape of a bioinformatics workflow: load data, QC it, process it, analyze it, and export results. Categories with a dedicated page are linked.
| 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 |
| 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 |
See also
- Custom Nodes Guide, build your own nodes
- Nodes and Connections, how nodes fit together in a graph