Citations

README.md

@@ -24,3 +24,39 @@ myco imports almost all of its code from other repos. Please see those specific
 * Turning VCFs into diff files: [parsevcf](https://github.com/lilymaryam/parsevcf)
 * Building UShER, Taxonium, and Nextstrain/Auspice trees: [tree-nine](https://github.com/aofarrel/tree-nine)
 * Determining why your sample spent 20 hours in the decontamination task: [FastQC-wdl](https://qa.dockstore.org/workflows/github.com/aofarrel/fastqc-wdl/fastqc)
+
+## Citations
+
+#### clockwork
+> Hunt, Martin, Brice Letcher, Kerri M. Malone, Giang Nguyen, Michael B. Hall, Rachel M. Colquhoun, Leandro Lima, et al. “Minos: Variant Adjudication and Joint Genotyping of Cohorts of Bacterial Genomes.” Genome Biology 23, no. 1 (December 2022): 147. https://doi.org/10.1186/s13059-022-02714-x.
+
+#### Cortex
+> Iqbal, Zamin, Mario Caccamo, Isaac Turner, Paul Flicek, and Gil McVean. “De Novo Assembly and Genotyping of Variants Using Colored de Bruijn Graphs.” Nature Genetics 44, no. 2 (February 2012): 226–32. https://doi.org/10.1038/ng.1028.
+
+#### fastp
+> Chen, Shifu. “Ultrafast One‐pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” iMeta 2, no. 2 (May 2023): e107. https://doi.org/10.1002/imt2.107.
+
+#### goleft
+> https://github.com/brentp/goleft
+
+#### matUtils
+> McBroome, Jakob, Bryan Thornlow, Angie S. Hinrichs, Alexander Kramer, Nicola De Maio, Nick Goldman, David Haussler, Russell Corbett-Detig, and Yatish Turakhia. “A Daily-Updated Database and Tools for Comprehensive Sars-Cov-2 Mutation-Annotated Trees.” Molecular Biology and Evolution 38, no. 12 (December 9, 2021): 5819–24. https://doi.org/10.1093/molbev/msab264.
+
+#### minimap2
+> Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Edited by Inanc Birol. Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191.
+
+#### samtools
+> Danecek, Petr, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience 10, no. 2 (January 29, 2021): giab008. https://doi.org/10.1093/gigascience/giab008.
+
+#### TBProfiler (version 4.4.2, database 2023-Mar-27)
+> Phelan, Jody E., Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Yaa E. A. Oppong, Susana Campino, Justin O’Grady, et al. “Integrating Informatics Tools and Portable Sequencing Technology for Rapid Detection of Resistance to Anti-Tuberculous Drugs.” Genome Medicine 11, no. 1 (December 2019): 41. https://doi.org/10.1186/s13073-019-0650-x.
+
+Note that some versions of this pipeline specifically uses Thiagen's fork of TBProfiler. The pinned version of this fork that I use itself uses TBProfiler version 4.4.2, database 2023-Jan-19.
+
+> Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. “Accelerating Bioinformatics Implementation in Public Health.” Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051.
+
+#### Trimmomatic
+> Bolger, Anthony M., Marc Lohse, and Bjoern Usadel. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30, no. 15 (August 1, 2014): 2114–20. https://doi.org/10.1093/bioinformatics/btu170.
+
+#### UShER
+> Turakhia, Yatish, Bryan Thornlow, Angie S. Hinrichs, Nicola De Maio, Landen Gozashti, Robert Lanfear, David Haussler, and Russell Corbett-Detig. “Ultrafast Sample Placement on Existing tRees (UShER) Enables Real-Time Phylogenetics for the SARS-CoV-2 Pandemic.” Nature Genetics 53, no. 6 (June 2021): 809–16. https://doi.org/10.1038/s41588-021-00862-7.