Citing Viridian - iqbal-lab-org/viridian GitHub Wiki

Please cite the preprint: https://doi.org/10.1101/2024.04.29.591666

Additionally, please cite the following tools, which are used by Viridian:

• MAFFT https://doi.org/10.1093/molbev/mst010
• minimap2 https://doi.org/10.1093/bioinformatics/bty191
• MUMmer https://doi.org/10.1371/journal.pcbi.1005944
• NGMerge https://doi.org/10.1186/s12859-018-2579-2
• Pysam https://github.com/pysam-developers/pysam
• Racon https://doi.org/10.1101/gr.214270.116
• ReadItAndKeep (if you use the option --decontam) https://doi.org/10.1093/bioinformatics/btac311
• SAMtools/BCFtools https://doi.org/10.1093/bioinformatics/btp352 https://doi.org/10.1093/gigascience/giab008