The use of Oxford Nanopore native barcoding for complete genome assembly

GigaScience

Volumn 6, Issue 3, 2017, Pages

  Bayliss, Sion C ^a   Hunt, Vicky L ^a   Yokoyama, Maho ^a   Thorpe, Harry A ^a   Feil, Edward J ^a  

^a Claverton Down   (United Kingdom)

Author keywords

Bacterial genomics; Hybrid assembly; Long read; MinION; Multiplexing; Native barcoding; Staphylococcus aureus; Whole genome sequencing

Indexed keywords

BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; DNA BARCODING; GENE LOSS; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC PARAMETERS; GENOME ASSEMBLY; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; NANOPORE; NONHUMAN; NOTE; PRIORITY JOURNAL; CLASSIFICATION; GENE LIBRARY; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; REPRODUCIBILITY; SPECIES DIFFERENCE;

BACTERIAL DNA;

DNA BARCODING, TAXONOMIC; DNA, BACTERIAL; GENOME, BACTERIAL; GENOMIC LIBRARY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; NANOPORES; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY;

EID: 85023167536     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1093/gigascience/gix001     Document Type: Note

References (22)

1. Glaser P, Martins-Simoes P, Villain A et al. Demography and Intercontinental spread of the USA300 communityacquired methicillin-resistant Staphylococcus aureus lineage. MBio 2016;7:e02183-15
2. Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 2015;12:733-5
3. Risse J, Thomson M, Patrick S et al. A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data. Gigascience 2015;4:60
4. Karlsson E, Lärkeryd A, Sj ödin A et al. Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci Rep 2015;5:11996
5. Madoui M-A, Engelen S, Cruaud C et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 2015;16:327
6. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014;30: 2114-20
7. Ip CLC, Loose M, Tyson JR et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research 2015;4:1-35
8. Oikonomopoulos S, Wang YC, Djambazian H et al. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 2016;6:31602
9. Bankevich A, Nurk S, Antipov D et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455-77
10. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-7
11. Diep BA, Gill SR, Chang RF et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 2006;367:731-9
12. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9
13. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60
14. Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25: 2078-9
15. ChaissonMJ, Tesler G, Smith T et al. Mapping singlemolecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012;13:238
16. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010;5:e11147
17. McKenna A, Hanna M, Banks E et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Res 2010;20:1297-303
18. Ye K, Schulz MH, Long Q et al. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009;25:2865-71
19. Kurtz S, Phillippy A, Delcher AL et al. Versatile and open software for comparing large genomes. Genome Biol 2004;5(2):R12
20. Shearer JES, Wireman J, Hostetler J et al. Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci. G3. 2011;1: 581-91
21. Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 2015;23: 110-20
22. Bayliss SC, Hunt VL, Yokoyama M et al. Supporting data for "The use of Oxford Nanopore native barcoding for complete genome assembly". GigaScience Database 2016; http://dx.doi.org/10.5524/100269