Note that Zorn/Bascet wraps many other software. Citing just Zorn/Bascet is not fair, so please cite the main paper + additional papers below depending on what features you have used
Citing Zorn/Bascet itself
Gourle H, Yakovenko I, Verma J, Dicken J, Albrecht F, Mazutis L, Normark J, Sheng N, Strömberg N, Löfstedt T, Carroll LM, Henriksson JM, Scalable single-cell metagenomic analysis with Bascet and Zorn, bioRxiv 2025.06.20.660799, https://doi.org/10.1101/2025.06.20.660799
SNP-analysis with cellsnp-lite
Xianjie Huang, Yuanhua Huang, Cellsnp-lite: an efficient tool for genotyping single cells, Bioinformatics, Volume 37, Issue 23, December 2021, Pages 4569–4571, https://doi.org/10.1093/bioinformatics/btab358
Donor deconvolution with vireo
Yuanhua Huang, Davis J. McCarthy, Oliver Stegle, Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference, Genome Biology, Volume 20, 273 (2019), https://doi.org/10.1186/s13059-019-1865-2
Alignment with BWA-MEM2
Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019, pp. 314-324. https://doi.org/10.1109/IPDPS.2019.00041
Alignment with STAR
Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, Volume 29, Issue 1, January 2013, Pages 15–21, https://doi.org/10.1093/bioinformatics/bts635
Alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, Volume 9, Issue 4, March 2012, Pages 357–359, https://doi.org/10.1038/nmeth.1923
Alignment with Minimap2
Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191
Read quality control with FastQC
Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Additional trimming with fastp (non-standard step)
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
Taxonomic classification with Kraken 2
Derrick E. Wood, Jennifer Lu, Ben Langmead, Improved metagenomic analysis with Kraken 2, Genome Biology, Volume 20, 257 (2019), https://doi.org/10.1186/s13059-019-1891-0
De novo assembly with SKESA
Souvorov A, Agarwala R, Lipman DJ, SKESA: strategic k-mer extension for scrupulous assemblies, Genome Biology, Volume 19, Issue 1, 153 (2018), https://doi.org/10.1186/s13059-018-1540-z
Assembly quality assessment with QUAST
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8, April 2013, Pages 1072–1075, https://doi.org/10.1093/bioinformatics/btt086
Genome annotation with Bakta
Oliver Schwengers, Lukas Jelonek, Marius A. Dieckmann, Sebastian Beyvers, Jochen Blom, Alexander Goesmann, Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification, Microbial Genomics, Volume 7, Issue 11, November 2021, 000685, https://doi.org/10.1099/mgen.0.000685
Antimicrobial resistance detection with ARIBA
Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris, ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads, Microbial Genomics, Volume 3, Issue 10, October 2017, 000131, https://doi.org/10.1099/mgen.0.000131
Antimicrobial resistance detection with AMRFinderPlus
Michael Feldgarden, Vyacheslav Brover, Narjol Gonzalez-Escalona, Jonathan G. Frye, Julie Haendiges, Daniel H. Haft, Maria Hoffmann, John B. Pettengill, Arjun B. Prasad, Glenn E. Tillman, Gregory H. Tyson, William Klimke, AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence, Scientific Reports, Volume 11, 12728 (2021), https://doi.org/10.1038/s41598-021-91456-0
Antimicrobial resistance detection with ABRicate
Seemann T, ABRicate: Mass screening of contigs for antimicrobial
and virulence genes. https://github.com/tseemann/abricate (Please also cite
the underlying database you used with --db.)
Biosynthetic gene clusters with GECCO
Laura M. Carroll, Martin Larralde, Jonas Simon Fleck, Ruby Ponnudurai, Sina Milanese, Elisa Cappio Barazzone, Georg Zeller, Accurate de novo identification of biosynthetic gene clusters with GECCO, bioRxiv 2021.05.03.442509, https://doi.org/10.1101/2021.05.03.442509