Below are citations of tools used in the pipeline that you should cite in your work when using this pipeline.
Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. (2020). The nf-core framework for community-curated bioinformatics pipelines. https://doi.org/10.1038/s41587-020-0439-x
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. (2017). doi: 10.1038/nbt.3820
- MultiQC
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. (2016). doi: 10.1093/bioinformatics/btw354.
Below are pipeline-specific tools, categorized by tools for Illumina preprocessing, Nanopore preprocessing, and general software tools.
- Fastp
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor. (2018). https://doi.org/10.1093/bioinformatics/bty560
- SPAdes
Andrey Prjibelski,Dmitry Antipov,Dmitry Meleshko,Alla Lapidus,Anton Korobeynikov. Using SPAdes De Novo Assembler. (2020). https://doi.org/10.1002/cpbi.102
- Bowtie2
Ben Langmead and Steven L Salzberg. Fast-gapped read alignment with bowtie2. (2012). https://doi.org/10.1038/nmeth.1923
- NanoPlot
De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. (2018). https://doi.org/10.1093/bioinformatics/bty149
- Porechop_ABI
Bonenfant Q, Noe L, Touzet H. Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming. (2022). doi:10.1101/2022.07.07.499093
- Flye
Kolmogorov M, Yuan J, Lin Y, Pevzner P. Assembly of long, error-prone reads using repeat graphs. (2019). doi:10.1038/s41587-019-0072-8
- minimap2
Li H. Minimap2: pairwise alignment for nucleotide sequences. (2018). https://doi.org/10.1093/bioinformatics/bty191
- Medaka
ONT Research. (2018). https://github.com/nanoporetech/medaka
- QUAST
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. (2013). doi:10.1093/bioinformatics/btt086
- metabat2 JGI Summarize Contigs
Dongwan D. Kang,1 Feng Li,2 Edward Kirton,1 Ashleigh Thomas,1 Rob Egan,1 Hong An,2 and Zhong Wang. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. (2019). https://doi.org/10.7717/peerj.7359
- Samtools
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. Twelve years of SAMtools and BCFtools. (2021). https://doi.org/10.1093/gigascience/giab008
- Sourmash
Brown CT, Irber L. (2016). Sourmash: a library for MinHash sketching of DNA. https://doi.org/10.21105/joss.00027
- Biopyton
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilcynzski B, de Hoon MJL. Biopython: freely available Python tools for computational molecular biology and bioinformatics. (2009). https://doi.org/10.1093/bioinformatics/btp163
- Prodigal
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. (2010). https://doi.org/10.1186/1471-2105-11-119
- DIAMOND
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. (2014). https://doi.org/10.1038/nmeth.3176
-
Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
-
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.
-
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.
-
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.