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danejo3 edited this page Dec 4, 2024 · 13 revisions

YEAT

YEAT (Your Everday Assembly Tool) is a platform designed for end-to-end processing of genome assemblies with support for multiple technologies and read types (both short and long). It utilizes a Snakemake workflow to orchestrate data quality control, execution of one or more assembly algorithms, post-assembly quality control, and visualization. YEAT can be configured for one or more samples, one or more assembly algorithms per sample, and one or more parameter sets per algorithm. Deployment in an HPC environment can accelerate workflow processing by executing independent tasks in parallel.

Read Types Supported Algorithms
Paired-end SPAdes1, MEGAHIT2, Unicycler3, PenguiN4, VelvetOptimiser5
Single-end SPAdes1, MEGAHIT2, Unicycler3, PenguiN4, VelvetOptimiser5
PacBio CLR (<20% error) Flye6, Canu7, Unicycler3
PacBio Corrected (<3% error) Flye6, Canu7, Unicycler3
PacBio HiFi (<1% error) Flye6, Canu7, Hifiasm8, Hifiasm-meta9, Unicycler3, MetaMDBG10
ONT Regular (<20% error) Flye6, Canu7, Unicycler3, MetaMDBG10
ONT Corrected (<3% error) Flye6, Canu7, Unicycler3, MetaMDBG10
ONT High-quality (<5% error) Flye6, Canu7, Unicycler3, MetaMDBG10

References

  1. Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020). Using SPAdes de novo assembler. Current Protocols in Bioinformatics, 70, e102. doi: 10.1002/cpbi.102
  2. Li, D., Luo, R., Liu, C.M., Leung, C.M., Ting, H.F., Sadakane, K., Yamashita, H. and Lam, T.W., 2016. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods.
  3. 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
  4. PenguiN: Jochheim A, Jochheim FA, Kolodyazhnaya A, Morice E, Steinegger M, Soeding J. Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs. Microbiome 12, 187, (2024)
  5. https://github.com/tseemann/VelvetOptimiser
  6. Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8
  7. Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017). doi:10.1101/gr.215087.116
  8. Cheng, H., Asri, M., Lucas, J., Koren, S., Li, H. (2024) Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21:967-970. https://doi.org/10.1038/s41592-024-02269-8
  9. Feng, X., Cheng, H., Portik, D. et al. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nat Methods 19, 671–674 (2022). https://doi.org/10.1038/s41592-022-01478-3
  10. Gaetan Benoit, Sebastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi and Christopher Quince High-quality metagenome assembly from long accurate reads with metaMDBG, Nature Biotechnology (2023).
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