Assembling Plant Genomes with Long-Read Sequencing

1. Provart NJ, Brady SM, Parry G et al (2021) Anno genominis XX: 20 years of Arabidopsis genomics. Plant Cell 33(4):832–845

   Article  Google Scholar 

2. Michael TP, Jupe F, Bemm F et al (2018) High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun 9(1):541

   Article  Google Scholar 

3. Michael TP, VanBuren R (2020) Building near-complete plant genomes. Curr Opin Plant Biol 54:26–33

   Article  CAS  Google Scholar 

4. Panda K, Slotkin RK (2020) Long-read cDNA sequencing enables a “gene-like” transcript annotation of transposable elements. Plant Cell 32(9):2687–2698

   Article  CAS  Google Scholar 

5. Shahid S, Slotkin RK (2020) The current revolution in transposable element biology enabled by long reads. Curr Opin Plant Biol 54:49–56

   Article  CAS  Google Scholar 

6. Schmidt MHW, Vogel A, Denton AK et al (2017) De novo assembly of a new Solanum pennellii accession using Nanopore sequencing. Plant Cell 29(10):2336–2348

   Article  CAS  Google Scholar 

7. Belser C, Istace B, Denis E et al (2018) Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat Plants 4(11):879–887

   Article  CAS  Google Scholar 

8. Della Coletta R, Qiu Y, Ou S et al (2021) How the pan-genome is changing crop genomics and improvement. Genome Biol 22(1):3

   Article  Google Scholar 

9. Lewin HA, Robinson GE, Kress WJ et al (2018) Earth BioGenome project: sequencing life for the future of life. Proc Natl Acad Sci U S A 115(17):4325–4333

   Article  CAS  Google Scholar 

10. Amarasinghe SL, Ritchie ME, Gouil Q (2021) long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data. GigaScience. 10(2):giab003

    Article  Google Scholar 

11. Li H. Seqtk: toolkit for processing sequences in FASTA/Q formats. Accessed 05 Mar 2021. https://github.com/lh3/seqtk

12. Fukasawa Y, Ermini L, Wang H et al (2020) LongQC: a quality control tool for third generation sequencing long read data. G3 (Bethesda) 10(4):1193–1196

    Article  CAS  Google Scholar 

13. Wick R. Porechop: adapter trimmer for Oxford Nanopore reads. Accessed: 2021-03-05. https://github.com/rrwick/Porechop

14. Wick R. Filtlong: quality filtering tool for long reads. Accessed: 2021-03-05. https://github.com/rrwick/Filtlong

15. Kolmogorov M, Yuan J, Lin Y et al (2019) Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5):540–546

    Article  CAS  Google Scholar 

16. Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100

    Article  CAS  Google Scholar 

17. Oxford Nanopore technologies. Medaka: sequence correction. Accessed: 2021-03-05. https://github.com/nanoporetech/medaka

18. Gurevich A, Saveliev V, Vyahhi N et al (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072–1075

    Article  CAS  Google Scholar 

19. Seppey M, Manni M, Zdobnov EM (2019) BUSCO: assessing genome assembly and annotation completeness. In: Kollmar M (ed) Gene prediction, Methods in Molecular Biology, vol 1962. Springer New York, New York, NY, pp 227–245

    Chapter  Google Scholar 

20. Wick RR, Judd LM, Holt KE (2019) Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 20(1):129

    Article  Google Scholar 

21. Murigneux V, Rai SK, Furtado A et al (2020) Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience 9(12):giaa146

    Article  Google Scholar 

22. Leger A, Leonardi T (2019) pycoQC, interactive quality control for Oxford Nanopore sequencing. J Open Source Soft 4(34):1236

    Article  Google Scholar 

23. Vaser R, Sović I, Nagarajan N et al (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27(5):737–746

    Article  CAS  Google Scholar 

24. Walker BJ, Abeel T, Shea T et al (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9(11):e112963

    Article  Google Scholar 

25. Bolger A, Scossa F, Bolger ME et al (2014) The genome of the stress tolerant wild tomato species Solanum pennellii. Nat Genet 46(9):1034–1038

    Article  CAS  Google Scholar 

26. Tørresen OK, Star B, Mier P et al (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 47(21):10994–11006

    Article  Google Scholar 

27. Lang D, Zhang S, Ren P et al (2020) Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific biosciences sequel II system and ultralong reads of Oxford Nanopore. GigaScience 9(12):giaa123

    Article  Google Scholar 

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