For publications

How to cite BioAnalysis.ca

If BioAnalysis.ca contributed to your research, please cite the platform and the underlying tools. A methods paragraph you can adapt is below.

Citation

BioAnalysis.ca (2026). Online 16S rRNA, ITS and bacterial whole-genome sequencing analysis platform. Edmonton, Alberta, Canada. https://bioanalysis.ca (accessed [date]).

BibTeX

@misc{bioanalysis_ca,
  title        = {{BioAnalysis.ca}: online 16S rRNA, ITS and bacterial WGS analysis platform},
  author       = {{BioAnalysis.ca}},
  year         = {2026},
  howpublished = {\url{https://bioanalysis.ca}},
  note         = {Edmonton, Alberta, Canada. Accessed: YYYY-MM-DD}
}

Methods paragraph for 16S rRNA analysis

Adapt this to your study. Replace the bracketed values with those in the Pipeline Parameters section of your report, which records the exact primers, truncation lengths and tool versions used for your data. Remove sentences for analyses you did not run; for example, beta diversity, PERMANOVA and ANCOM-BC2 apply to multi-sample projects only.

16S rRNA gene amplicon data were analyzed with BioAnalysis.ca (https://bioanalysis.ca; accessed [date]). Primer sequences ([forward primer]/[reverse primer]) were removed with Cutadapt v5.2 (Martin, 2011), discarding reads without the primer. Reads were quality-filtered and truncated ([R1] bp and [R2] bp), denoised into amplicon sequence variants (ASVs), merged and screened for chimeras with DADA2 v1.34.0 (Callahan et al., 2016) in R v4.4.2. Taxonomy was assigned with the naive Bayesian classifier (Wang et al., 2007) against the SILVA v138.2 reference database (Quast et al., 2013), with exact-match species assignment. ASVs were aligned with MAFFT v7.525 (Katoh & Standley, 2013) and a phylogeny was inferred with FastTree v2.2.0 (Price et al., 2010). Alpha diversity was measured with the Shannon, Simpson and Chao1 indices and Faith's phylogenetic diversity (Faith, 1992). Beta diversity was calculated as Bray-Curtis and Jaccard distances, visualized by principal coordinates analysis and tested with PERMANOVA using 999 permutations (Anderson, 2001). Differentially abundant taxa between groups were identified with ANCOM-BC2 (Lin & Peddada, 2024). Metabolic pathway abundances were predicted with PICRUSt2 v2.5.3 (Douglas et al., 2020).

For ITS data, replace SILVA with UNITE v9.0 (Nilsson et al., 2019) and remove the phylogeny, Faith's PD and PICRUSt2 sentences.

References for the underlying tools

  1. Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecology. 2001;26:32–46.
  2. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods. 2016;13:581–583.
  3. Douglas GM, Maffei VJ, Zaneveld JR, et al. PICRUSt2 for prediction of metagenome functions. Nature Biotechnology. 2020;38:685–688.
  4. Faith DP. Conservation evaluation and phylogenetic diversity. Biological Conservation. 1992;61:1–10.
  5. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution. 2013;30:772–780.
  6. Lin H, Peddada SD. Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures. Nature Methods. 2024;21:83–91.
  7. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10–12.
  8. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
  9. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research. 2013;41:D590–D596.
  10. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology. 2007;73:5261–5267.
  11. Nilsson RH, Larsson KH, Taylor AFS, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research. 2019;47:D259–D264.

Questions

Reviewers asking about a parameter or method? Email [email protected] or read the amplicon pipeline documentation and the 16S pipeline overview.