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mk-kondo/mikrokondo: Citations

nf-core

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. PubMed PMID: 32055031.

Nextflow

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. PubMed PMID: 28398311.

Pipeline tools

  • Abricate

    Seemann T, Abricate, Github https://github.com/tseemann/abricate

  • Bakta

    Schwengers O., Jelonek L., Dieckmann M. A., Beyvers S., Blom J., Goesmann A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). https://doi.org/10.1099/mgen.0.000685

  • Bandage

    Wick R.R., Schultz M.B., Zobel J. & Holt K.E. (2015). Bandage: interactive visualisation of de novo genome assemblies. Bioinformatics, 31(20), 3350-3352.

  • CheckM

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043-1055.

  • ECTyper

    Bessonov K, Laing C, Robertson J, Yong I, Ziebell K, Gannon VPJ, Nichani A, Arya G, Nash JHE, Christianson S. ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb Genom. 2021 Dec;7(12):000728. doi: 10.1099/mgen.0.000728. PMID: 34860150; PMCID: PMC8767331.

  • FastP

    Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884-i890, https://doi.org/10.1093/bioinformatics/bty560

  • FastQC

  • Flye

    Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner "metaFlye: scalable long-read metagenome assembly using repeat graphs", Nature Methods, 2020 doi:s41592-020-00971-x

  • GTDB

    Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785–D794, https://doi.org/10.1093/nar/gkab776

  • Kleborate

    Lam, MMC. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications (2021)

  • Kraken2

    Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0

  • LisSero

    Doumith et al. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22

  • Mash

    Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

  • Medaka

  • Minimap2

    Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. doi:10.1093/bioinformatics/btab705

  • mlst

    Seemann T, mlst Github https://github.com/tseemann/mlst

  • mob-suite

    Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom. 2018 Aug;4(8):e000206. doi: 10.1099/mgen.0.000206. Epub 2018 Jul 27. PMID: 30052170; PMCID: PMC6159552.

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

  • Pilon

    Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963

  • Quast

    Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich, Versatile genome assembly evaluation with QUAST-LG, Bioinformatics (2018) 34 (13): i142-i150. doi: 10.1093/bioinformatics/bty266 First published online: June 27, 2018

  • Racon

    Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18. PMID: 28100585; PMCID: PMC5411768.

  • Samtools

    Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

  • Seqtk

  • Shigatyper

    Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)

  • Sistr

    The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101

  • Spades

    Bankevich A., Nurk S., Antipov D., Gurevich A., Dvorkin M., Kulikov A. S., Lesin V., Nikolenko S., Pham S., Prjibelski A., Pyshkin A., Sirotkin A., Vyahhi N., Tesler G., Alekseyev M. A., Pevzner P. A. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012

  • Spatyper

    Jose Francisco Sanchez-Herrero, & mjsull. (2020). spaTyper: Staphylococcal protein A (spa) characterization pipeline (v0.3.1). Zenodo. https://doi.org/10.5281/zenodo.4063625

  • StarAMR

    Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Domselaar GV, Reid-Smith RJ, Mulvey MR. Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr. Microorganisms. 2022; 10(2):292. https://doi.org/10.3390/microorganisms10020292

  • Unicycler

    Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

  • Singularity

    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. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.