Kaiju
Taxonomic ClassificationKaiju is a protein-level metagenomic classifier that translates DNA reads into amino acid sequences and matches them against a reference protein database using the Burrows-Wheeler transform (BWT). [1]
How to Obtain Output Model File
Below is a brief workflow the team ran to obtain the output model examples we present on the tools page.
Input
FASTQ/FASTA files (single-end or paired-end reads)
Output
Tab-separated classification with taxon IDs, plus summary tables at each taxonomic rank
conda install -c bioconda kaiju
Docker image: quay.io/biocontainers/kaiju:1.10.1--h43eeafb_0
Sample 1 gut metagenome reads (200K subset) classified with Kaiju against a curated gut microbiome Database (644 representative/reference genomes from NCBI RefSeq).
- 1
Download reads from NCBI SRA
prefetch SRR14092310 && fasterq-dump SRR14092310 -O /data --split-files && gzip /data/SRR14092310_*.fastq
- 2
Subset to 200K read pairs
zcat SRR14092310_1.fastq.gz | head -800000 > subset_R1.fastq && zcat SRR14092310_2.fastq.gz | head -800000 > subset_R2.fastq
200K subset keeps the output under IntMeta's 50 MB upload limit.
- 3
Run Kaiju classification
kaiju -t nodes.dmp -f kaiju_db_gut.fmi -i subset_R1.fastq -j subset_R2.fastq -o kaiju_raw.tsv -z 12
- 4
Add taxon names
kaiju-addTaxonNames -t nodes.dmp -n names.dmp -i kaiju_raw.tsv -o kaiju_output.tsv -r superkingdom,phylum,class,order,family,genus,species -u
kaiju_output.tsv to IntMetaMaterials Used
Sample Output Files
Download the output files used in the tool page demos. You can upload these directly to IntMeta to explore the visualizations.
Single & Comparison
Group Analysis
Charts Reference
Detailed descriptions for all 30 visualizations generated by Kaiju in IntMeta.
distribution
Bar chart of the top organisms ranked by read count from Kaiju's protein-level classification. Because Kaiju translates reads to amino acids before matching, it can detect divergent organisms that nucleotide k-mer methods miss.
composition
Pie/donut chart showing the top taxa as a percentage of their combined read count at the selected rank, derived from Kaiju's BWT protein-level assignments.
richness
Counts every distinct organism with at least one assigned read at each major rank (Domain through Species). Protein-level classification tends to detect additional divergent or novel taxa compared to DNA k-mer tools.
diversity
Alpha diversity indices computed from per-taxon read-count proportions: Shannon H = −Σ(pᵢ · ln pᵢ), Simpson D = 1 − Σ(nᵢ(nᵢ−1))/(N(N−1)), and Pielou's evenness J = H / ln(richness). Measures community richness and evenness from Kaiju abundance data.
multilevel-composition
Stacked bar chart with the top taxa (by read count) at each major rank; remaining taxa grouped as 'Other'. Reveals compositional shifts from Phylum to Species level.
dependency-wheel
Chord diagram linking parent to child taxa across ranks from the Kaiju lineage output. Connection thickness is proportional to shared read count; edges below the minimum coverage threshold are filtered.
sankey-flow
Sankey flow diagram showing how reads distribute from higher to lower taxonomic ranks through the Kaiju classification hierarchy. Band width equals read count; low-coverage edges are removed.
comp-grouped-abundance
Grouped bar chart placing the top taxa from each sample side by side at the selected rank. Each group contains one bar per sample, colored by sample identity, enabling direct visual comparison of absolute read counts for the same organism across Kaiju-classified samples.
comp-relative-abundance
100% stacked bar chart where each bar represents one sample and segments show the proportional contribution of each taxon. Useful for comparing community composition when samples have very different sequencing depths, since all bars are normalized to the same height.
comp-abundance-heatmap
Color-matrix heatmap with taxa on one axis and samples on the other. Cell color intensity is proportional to read abundance at the selected rank. Hierarchical clustering on both axes groups similar samples and co-occurring taxa together.
comp-diversity-indices
Multi-panel chart displaying Shannon entropy, Simpson diversity, Observed Richness, and Pielou's Evenness for each sample on its own y-axis scale. Enables quick cross-sample comparison of alpha diversity without scale distortion.
comp-shared-taxa
Venn diagram showing the count of taxa that are shared between samples versus taxa exclusive to each individual sample. Computed at the selected taxonomic rank using presence/absence of reads ≥ 1.
group-alpha-diversity
Boxplots of Shannon entropy, Simpson diversity, Observed Richness, and Pielou's Evenness per group. Each box summarizes within-group variation. Kruskal-Wallis p-values test for significant differences between groups.
group-pcoa
Principal Coordinates Analysis (PCoA) on Bray-Curtis dissimilarity matrix. Points are colored by group assignment with 95% confidence ellipses. Axis labels show the percentage of variance explained by each coordinate.
group-nmds
Non-metric Multidimensional Scaling (NMDS) ordination with stress value displayed. Points colored by group with confidence ellipses. Lower stress (<0.2) indicates a good representation of the original distances in 2D.
group-distance-boxplots
Boxplots of within-group vs between-group Bray-Curtis distances. PERMANOVA R² and p-value quantify the fraction of variance explained by grouping. ANOSIM R statistic measures the degree of group separation.
group-relative-abundance
Group-averaged relative abundance as 100% stacked bars at the selected taxonomic rank. Each bar shows the mean proportional composition across all samples in the group, enabling direct group-level comparison.
group-differential-abundance
Bar chart of taxa with significant abundance differences between groups (Kruskal-Wallis test, Benjamini-Hochberg FDR correction). Color indicates which group has higher abundance. Only taxa passing the significance threshold are shown.
group-lefse
LEfSe (Linear Discriminant Analysis Effect Size) biomarker chart. Horizontal bars show LDA scores for taxa that significantly discriminate between groups. Higher LDA scores indicate stronger association with the respective group.
group-shared-taxa
Venn diagram showing shared and unique taxa across experimental groups. Each group's taxa set is the union of all taxa detected in any sample belonging to that group. Click regions to view the specific taxa list with read counts.
group-classification
Stacked column chart showing mean classified vs unclassified reads per experimental group. Tooltip shows percentage breakdown and sample count per group.
group-distribution
Grouped column chart showing mean read counts for top N taxa at the selected taxonomic level, grouped by experimental group. Enables comparison of taxonomic abundance patterns between groups.
group-heatmap
Heatmap of mean log₁₀-transformed read counts per experimental group (columns) and taxa (rows). Color intensity reflects abundance, allowing quick visual comparison of taxonomic profiles across groups.
rarefaction
Rarefaction curve plotting observed taxa vs subsampled read depth at the selected rank. Computed analytically using the hypergeometric expectation. A curve that plateaus indicates sufficient sequencing depth; a curve still rising suggests under-sampling.
rank-abundance
Rank-abundance curve (Whittaker plot) with taxa ranked by decreasing relative abundance on a logarithmic y-axis. The curve's length along the x-axis reflects richness, while the slope indicates evenness — a steep drop means a few taxa dominate.
comp-rarefaction
Overlaid rarefaction curves for all uploaded samples. Enables visual comparison of sequencing effort and taxonomic saturation across samples.
comp-rank-abundance
Overlaid rank-abundance curves for all uploaded samples. Steeper curves indicate more uneven communities dominated by fewer taxa.
group-taxonomic-sunburst
Interactive sunburst displaying the full taxonomic hierarchy as concentric rings. LEfSe biomarker nodes are colored by their enriched group; non-significant nodes are gray. Click any ring segment to drill down.
group-volcano
Volcano plot: log₂ fold-change (x) vs −log₁₀ adjusted p-value (y). Points above the horizontal line pass significance (BH FDR). Colored points are significantly enriched in the respective group.
comp-classification
Stacked bar chart showing total classified vs unclassified reads per sample. Enables quick comparison of classification rates across samples — large unclassified fractions may indicate novel organisms or database limitations.