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ilypopv merged 6 commits into from
Oct 20, 2026
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docs(paper): update feature comparison table formatting and text in paper.md #29

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docs(paper): remove inline code formatting from script names in summa…
ilypopv Oct 20, 2026
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docs(paper): wrap long script names in markdown table for better read…
ilypopv Oct 20, 2026
afccb6a
docs(paper): update markdown table formatting and phrasing for clarity
ilypopv Oct 20, 2026
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docs(paper): shorten kreport2krona description in summary table
ilypopv Oct 20, 2026
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style(paper): adjust markdown table column alignment for better reada…
ilypopv Oct 20, 2026
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style: use and symbol
ilypopv Oct 20, 2026
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4 changes: 2 additions & 2 deletions paper/paper.md
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Expand Up @@ -32,9 +32,9 @@ Comparative metagenomics and microbiome studies depend fundamentally on cross-sa
The table below summarizes, based on the official documentation of each project, how `KrakenParser` relates to `KrakenTools` [@lu2022kraken], `Pavian` [@breitwieser2020pavian], and `spideog` [@manguy2020spideog] along the axes of supported input, batch processing, diversity calculations, visualization, and mode of use.

| Feature | `KrakenParser` | `KrakenTools` | `Pavian` | `spideog` |
|---|---|---|---|---|
|:--|:---|:----|:---|:---|
| Supported input | Kraken2 reports and Bracken abundance-estimation output (Kraken2-style format) | Kraken 1, Kraken 2, KrakenUniq, and Bracken reports; several scripts also accept raw FASTA/FASTQ read files | Kraken, KrakenUniq, Kraken 2, Centrifuge, and MetaPhlAn-style reports, plus BAM alignments for its viewer | Kraken2 and Bracken reports |
| Batch processing | Single CLI invocation ingests a directory of reports and produces rank-specific cross-sample matrices | `combine_kreports.py`/`combine_mpa.py` merge multiple reports, but each script is invoked and chained by the user; no unified multi-sample driver | Multi-sample comparison view within the interactive browser session; no scriptable or headless batch mode | `combine-abundances`/`combine-trees` subcommands merge multiple reports into one CSV or Newick file per invocation |
| Batch processing | Single CLI invocation ingests a directory of reports and produces rank-specific cross-sample matrices | `combine_kreports.py` & `combine_mpa.py` merge multiple reports, but each script is invoked and chained by the user; no unified multi-sample driver | Multi-sample comparison view within the interactive browser session; no scriptable or headless batch mode | `combine-abundances` / `combine-trees` subcommands merge multiple reports into one CSV or Newick file per invocation |
| Diversity calculations | Built-in alpha (Shannon, Pielou, Chao1, computed on raw counts) and beta (Bray-Curtis, Jaccard, with rarefaction) diversity | `DiversityTools` add-on scripts: alpha (Shannon, Berger-Parker, Simpson, inverse Simpson, Fisher), one sample at a time, and beta (Bray-Curtis only); neither includes rarefaction | None | None |
| Visualization | Stacked bar plots, streamgraphs, and clustermaps rendered as static figures | None built in; `kreport2krona.py` exports a Krona-compatible text file for rendering with the external Krona tool | Interactive Sankey diagrams, sample overview plots, and a BAM alignment pileup viewer rendered in the browser | None |
| Mode of use | Single CLI command for the full pipeline, or modular subcommands, suited to scripted/headless execution (HPC, CI) | Suite of independent Python CLI scripts, each run and chained manually by the user | Interactive R/Shiny web application (local install or Docker), designed for exploratory use rather than headless automation | Standalone compiled CLI binary performing one format-conversion operation per invocation |
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