Citation

If you use Hybracter, please cite the manuscript along with core dependencies (they are also our tools!):

Hybracter Manuscript * George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J. Roach, Bhavya Papudeshi, Louise M Judd, Anna E Sheppard, Robert A Edwards, Sarah Vreugde - Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies. (2024) Microbial Genomics doi: https://doi.org/10.1099/mgen.0.001244.

Plassembler: * Bouras G., Sheppard A.E., Mallawaarachchi V., Vreugde S., Plassembler: an automated bacterial plasmid assembly tool, Bioinformatics, Volume 39, Issue 7, July 2023, btad409, https://doi.org/10.1093/bioinformatics/btad409.

Dnaapler: * George Bouras, Susanna R. Grigson, Bhavya Papudeshi, Vijini Mallawaarachchi, Michael J. Roach (2024). Dnaapler: A tool to reorient circular microbial genomes. Journal of Open Source Software, 9(93), 5968, https://doi.org/10.21105/joss.05968.

Ryan Wick et al's Assembling the perfect bacterial genome paper, which provided the intellectual framework for hybracter: * Wick RR, Judd LM, Holt KE (2023) Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS Comput Biol 19(3): e1010905. https://doi.org/10.1371/journal.pcbi.1010905

I would also recommend citing Hybracter's other dependencies if you can where they are used:

Flye: * Kolmogorov, M., Yuan, J., Lin, Y. et al. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37, 540–546 (2019). https://doi.org/10.1038/s41587-019-0072-8

Snaketool: * Roach MJ, Pierce-Ward NT, Suchecki R, Mallawaarachchi V, Papudeshi B, Handley SA, et al. (2022) Ten simple rules and a template for creating workflows-as-applications. PLoS Comput Biol 18(12): e1010705. https://doi.org/10.1371/journal.pcbi.1010705

Trimnami: * Roach MJ. (2023) Trimnami. https://github.com/beardymcjohnface/Trimnami.

Filtlong: * Wick RR (2018) Filtlong. https://github.com/rrwick/Filtlong.

Porechop and Porechop_abi: * Quentin Bonenfant, Laurent Noé, Hélène Touzet, Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbac085, https://doi.org/10.1093/bioadv/vbac085 * Wick RR (2017) https://github.com/rrwick/Porechop.

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

ALE: * Scott C. Clark, Rob Egan, Peter I. Frazier, Zhong Wang, ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies, Bioinformatics, Volume 29, Issue 4, February 2013, Pages 435–443, https://doi.org/10.1093/bioinformatics/bts723

Medaka: * Oxford Nanopore Technologies, Medaka. https://github.com/nanoporetech/medaka.

Pyrodigal: * Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296, https://doi.org/10.21105/joss.04296.

Polypolish: * Wick RR, Holt KE (2022) Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol 18(1): e1009802. https://doi.org/10.1371/journal.pcbi.1009802.

Pypolca: * Bouras G, Judd LM, Edwards RA, Vreugde S, Stinear TP, Wick RR (2024) How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. bioRxiv 2024.03.07.584013; doi: https://doi.org/10.1101/2024.03.07.584013. * Zimin AV, Salzberg SL (2020) The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput Biol 16(6): e1007981. https://doi.org/10.1371/journal.pcbi.1007981.

Snakemake: * Mölder F, Jablonski KP, Letcher B et al. Sustainable data analysis with Snakemake [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2021, 10:33 (https://doi.org/10.12688/f1000research.29032.1).