Citations

Credits

nf-core/pathogensurveillance was written by:

Zachary S. L. Foster1, Martha Sudermann2, Camilo Parada-Rojas2, Fernanda Iruegas-Bocardo2, Ricardo Alcalá-Briseño2, Logan K. Blair 1, Alexandra J Weisberg2, Jeff H. Chang2, and Niklaus J. Grünwald1

1Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97331, USA

2Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #pathogensurveillance channel (you can join with this invite).

Citations

Note: these citations are for all possible programs that may be used by pathogensurveillance. The final report will only present citations of programs used in the current run.

Andrews, Simon et al. 2010. “FastQC: A Quality Control Tool for High Throughput Sequence Data.” Cambridge, United Kingdom.
Bayliss, Sion C, Harry A Thorpe, Nicola M Coyle, Samuel K Sheppard, and Edward J Feil. 2019. “PIRATE: A Fast and Scalable Pangenomics Toolbox for Clustering Diverged Orthologues in Bacteria.” Gigascience 8 (10): giz119.
Brown, C Titus, and Luiz Irber. 2016. “Sourmash: A Library for MinHash Sketching of DNA.” Journal of Open Source Software 1 (5): 27.
Bushnell, Brian. 2014. “BBMap: A Fast, Accurate, Splice-Aware Aligner.”
Chen, Shifu. 2023. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” Imeta 2 (2): e107.
Crusoe, Michael R, Hussien F Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, et al. 2015. “The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis.” F1000Research 4.
Danecek, Petr, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, et al. 2011. “The Variant Call Format and VCFtools.” Bioinformatics 27 (15): 2156–58.
Danecek, Petr, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, et al. 2021. “Twelve Years of SAMtools and BCFtools.” Gigascience 10 (2): giab008.
Di Tommaso, Paolo, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, and Cedric Notredame. 2017. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology 35 (4): 316–19.
Distribution, Anaconda Software. 2016. “Computer Software.” Vers. 4: 2–2.
Dylus, David, Adrian Altenhoff, Sina Majidian, Fritz J Sedlazeck, and Christophe Dessimoz. 2024. “Inference of Phylogenetic Trees Directly from Raw Sequencing Reads Using Read2Tree.” Nature Biotechnology 42 (1): 139–47.
Eggertsson, Hannes P, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, et al. 2017. “Graphtyper Enables Population-Scale Genotyping Using Pangenome Graphs.” Nature Genetics 49 (11): 1654–60.
Ewels, Philip A, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, and Sven Nahnsen. 2020. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology 38 (3): 276–78.
Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–48.
Garrison, Erik, Zev N Kronenberg, Eric T Dawson, Brent S Pedersen, and Pjotr Prins. 2022. “A Spectrum of Free Software Tools for Processing the VCF Variant Call Format: Vcflib, Bio-Vcf, Cyvcf2, Hts-Nim and Slivar.” PLoS Computational Biology 18 (5): e1009123.
Grüning, Björn, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster, and Bioconda Team. 2018. “Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences.” Nature Methods 15 (7): 475–76.
Kamvar, Zhian N, Javier F Tabima, and Niklaus J Grünwald. 2014. “Poppr: An r Package for Genetic Analysis of Populations with Clonal, Partially Clonal, and/or Sexual Reproduction.” PeerJ 2: e281.
Katoh, Kazutaka, Kazuharu Misawa, Kei-ichi Kuma, and Takashi Miyata. 2002. “MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform.” Nucleic Acids Research 30 (14): 3059–66.
Kolmogorov, Mikhail, Jeffrey Yuan, Yu Lin, and Pavel A Pevzner. 2019. “Assembly of Long, Error-Prone Reads Using Repeat Graphs.” Nature Biotechnology 37 (5): 540–46.
Kurtzer, Gregory M, Vanessa Sochat, and Michael W Bauer. 2017. “Singularity: Scientific Containers for Mobility of Compute.” PloS One 12 (5): e0177459.
Li, Heng. 2011. “Tabix: Fast Retrieval of Sequence Features from Generic TAB-Delimited Files.” Bioinformatics 27 (5): 718–19.
Li, Heng, and Richard Durbin. 2009. “Fast and Accurate Short Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 25 (14): 1754–60.
Manni, Mosè, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, and Evgeny M Zdobnov. 2021. “BUSCO Update: Novel and Streamlined Workflows Along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.” Molecular Biology and Evolution 38 (10): 4647–54.
Mikheenko, Alla, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, and Alexey Gurevich. 2018. “Versatile Genome Assembly Evaluation with QUAST-LG.” Bioinformatics 34 (13): i142–50.
Nguyen, Lam-Tung, Heiko A Schmidt, Arndt Von Haeseler, and Bui Quang Minh. 2015. “IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies.” Molecular Biology and Evolution 32 (1): 268–74.
“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute.
Prjibelski, Andrey, Dmitry Antipov, Dmitry Meleshko, Alla Lapidus, and Anton Korobeynikov. 2020. “Using SPAdes de Novo Assembler.” Current Protocols in Bioinformatics 70 (1): e102.
Qin, Qi-Long, Bin-Bin Xie, Xi-Ying Zhang, Xiu-Lan Chen, Bai-Cheng Zhou, Jizhong Zhou, Aharon Oren, and Yu-Zhong Zhang. 2014. “A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights.” Journal of Bacteriology 196 (12): 2210–15.
R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Sayers, Eric W, Evan E Bolton, J Rodney Brister, Kathi Canese, Jessica Chan, Donald C Comeau, Ryan Connor, et al. 2022. “Database Resources of the National Center for Biotechnology Information.” Nucleic Acids Research 50 (D1): D20.
Schwengers, Oliver, Lukas Jelonek, Marius Alfred Dieckmann, Sebastian Beyvers, Jochen Blom, and Alexander Goesmann. 2021. “Bakta: Rapid and Standardized Annotation of Bacterial Genomes via Alignment-Free Sequence Identification.” Microbial Genomics 7 (11): 000685.
Shen, Wei, Shuai Le, Yan Li, and Fuquan Hu. 2016. “SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/q File Manipulation.” PloS One 11 (10): e0163962.
Van der Auwera, Geraldine A, and Brian D O’Connor. 2020. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media.
Veiga Leprevost, Felipe da, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, et al. 2017. “BioContainers: An Open-Source and Community-Driven Framework for Software Standardization.” Bioinformatics 33 (16): 2580–82.