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BIOZIG
BioZig (BZ) CLI COMMAND LINE INTERFACE

The BZ Command Line Interface (biozig) provides a lightning-fast, zero-dependency binary for executing biological algorithms directly from the terminal.

BZ does not guess. BZ does not approximate. If a graph traversal cannot prove its cycle resolution, it fails. If a structural parser drops precision in coordinate translation, it fails. BZ is built on the premise that biological data must be exactly represented and deterministically verified before any complex algorithm is allowed to run.

Global Options
Standard POSIX-style flags across all commands
  • -i, --input <path> The absolute or relative path to the input file. You can also specify - to pipe data into BZ from stdin.
  • -o, --output <path> The file destination for the analysis results. If omitted, BZ outputs directly to stdout.
  • -f, --format <type> The output format for standard streams (text or json).
  • -t, --threads <num> Set the number of CPU threads used for multi-threading heavily parallelizable computations.
  • -r, --report <path> Generates a human-readable compiled report combining graphs, statistics, and runtimes.
  • -p, --plot Generates an inline ANSI/ASCII visualization plot directly in your terminal output.
  • -h, --help Show the detailed help message for any domain or subcommand.

Domains & Commands

biozig genomics
Sequence alignment, mapping, and analysis
Commands: align, index, parse, kmer, hmm, gibbs, suffix-tree, assembly, msa.
biozig analytics
Statistical models, matrix decompositions, and clustering
Commands: pca, nmf, mds, descriptive, correlation, hypothesis, distributions, multiple_testing, regression, survival, dispersion, biology, enrichment, metrics, umap, tsne, kmeans, dbscan, hierarchical, node2vec, spectral, sparse, svd, spia, markov, kmer_stats.
biozig structural
3D protein structures and interactions
Commands: atom, residue, chain, model, assembly, geometry, contacts, surfaces, pockets, dock, dynamics, anm, threading, rotamers, ingestion.
biozig cellular
Single-cell tools for dimensionality reduction and clustering
Commands: umap, tsne, kmeans, zinb, pseudotime.
biozig systems
Systems biology and network analysis
Commands: maxflow, motif, layout, centrality, community, network, metabolism, signaling, pathway, regulation, ontology, knowledgegraph, sbml, biopax, gpml.
biozig population
Population genetics analysis
Commands: gwas, admixture, ibd, hwe, ld, selection, epi, impute, fstats, vstats, vmatch, vfilter.
biozig evolutionary
Phylogenetics and evolutionary models
Commands: nj, upgma, mle, parsimony, mcmc, bootstrap, nni, spr, stats, rf-distance, parse-newick, parse-nexus, parse-phyloxml.
biozig reporting
Automated reporting and publication exports
Commands: html, latex, manuscript, markdown, pdf, supplement.
biozig visualize
Render beautiful biological data and plots
Commands: dashboards, network, omics, phylogeny, publication, sequence, structure.

Unix Pipeline Integration Examples

Streaming JSON to JQ
$ biozig analytics pca -i 1M_cells.mtx -f json | jq '.eigenvalues[] | select(.variance > 0.05)'
Compressing Aligned Output on the Fly
$ biozig genomics align -i reads.fastq --ref genome.fa | gzip > output.bam
Visualizing Terminal Outputs Instantly
$ biozig structural contacts -i viral_envelope.mmcif -p
*(Prints an ASCII topological map of the viral envelope contacts before exiting)*