References for the programs and frameworks used in the Metatropics pipeline.
Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820.
Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014 Mar 1;239:Article 2. doi: 10.5555/2600239.2600241.
Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459.
Dorado (POD5 basecalling + demultiplexing)
Oxford Nanopore Technologies. Dorado (basecalling software). https://github.com/nanoporetech/dorado (cite the release you used; follow ONT’s documentation for your chemistry).
BBMap / BBTools (rarefaction subsampling)
Bushnell B, Rood J, Singer E. BBMerge – Accurate paired shotgun read merging via overlap. PLOS ONE. 2017 Oct 26;12(10):e0185056. doi: 10.1371/journal.pone.0185056.
NanoPlot (read QC plots)
De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149.
fastplong (read trimming / filtering)
Chen S. fastplong: ultrafast preprocessing and quality control for long-read sequencing data (Nanopore, PacBio, etc.). https://github.com/OpenGene/fastplong (cite the release you used).
minimap2 (host mapping / depletion)
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191.
samtools (BAM sorting + BAM→FASTQ extraction)
Li H, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-2079. doi: 10.1093/bioinformatics/btp352.
Virasign (viral classification)
Jansen, D., & Vercauteren, K. (2026). Virasign: A viral taxonomic classification tool designed for nanopore sequencing data (v0.0.6). Zenodo. doi: 10.5281/zenodo.18387008.
Clair3 (per-virus variant calling)
Zheng Z, Li S, Su J, Leung AW-S, Lam TTY, Luo R. Clair3: a deep learning based variant caller for long-read sequencing data. (Project homepage / code) https://github.com/HKU-BAL/Clair3.
bcftools (draft consensus calling)
Danecek P, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi: 10.1093/gigascience/giab008.