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org/10.1101/gr.214346.116
43. Tadpole Guide. https://jgi.doe.gov/dataand-tools/bbtools/bb-tools-user-guide/tad
pole-guide/
44. Bankevich A, Nurk S, Antipov D, Gurevich
AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,
Sirotkin AV, Vyahhi N, Tesler G, Alekseyev
MA, Pevzner PA (2012) SPAdes: a new
genome assembly algorithm and its applications to single-cell sequencing. J Comput
Biol 19(5):455–477. https://doi.org/10.
1089/cmb.2012.0021
45. Chevreux B MIRA—The Genome and Transcriptome Assembler and Mapper. https://
github.com/bachev/mira
46. Li H seqtk. https://github.com/lh3/seqtk
47. Shen W, Le S, Li Y, Hu F (2016) SeqKit: a
cross-platform and ultrafast toolkit for
FASTA/Q file manipulation. PLoS One 11
(10):e0163962. https://doi.org/10.1371/
journal.pone.0163962
48. Wick RR, Judd LM, Gorrie CL, Holt KE
(2017) Unicycler: resolving bacterial genome
assemblies from short and long sequencing
reads. PLoS Comput Biol 13(6):e1005595.
https://doi.org/10.1371/journal.pcbi.
1005595
49. Li H (2016) Minimap and miniasm: fast
mapping and de novo assembly for noisy
long
sequences.
Bioinformatics
32
(14):2103–2110. https://doi.org/10.1093/
bioinformatics/btw152
50. Koren S, Walenz BP, Berlin K, Miller JR,
Bergman NH, Phillippy AM (2017) Canu:
scalable and accurate long-read assembly via
adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736
51. Kolmogorov M, Yuan J, Lin Y, Pevzner PA
(2019) Assembly of long, error-prone reads
using repeat graphs. Nat Biotechnol 37
(5):540–546.
https://doi.org/10.1038/
s41587-019-0072-8
52. Wick RR, Holt KE (2019) Benchmarking of
long-read assemblers for prokaryote whole
genome sequencing. F1000Res 8:2138.
https://doi.org/10.12688/f1000research.
21782.1
53. Vaser R, Sovic ´ I, Nagarajan N, S ˇ ikic ´ M (2017)
Fast and accurate de novo genome assembly
from long uncorrected reads. Genome Res 27
(5):737–746
54. Oxford Nanopore Technologies (2018)
Medaka.
https://github.com/
nanoporetech/medaka
55. Simpson J Nanopolish. https://github.com/
jts/nanopolish
56. De Maio N, Shaw LP, Hubbard A, George S,
Sanderson ND, Swann J, Wick R,
AbuOun M, Stubberfield E, Hoosdally SJ,
Crook DW, Peto TEA, Sheppard AE, Bailey
MJ, Read DS, Anjum MF, Walker AS,
Stoesser N, On Behalf Of The Rehab C
(2019) Comparison of long-read sequencing
technologies in the hybrid assembly of complex bacterial genomes. Microb Genom 5(9):
e000294. https://doi.org/10.1099/mgen.
0.000294
57. Crusoe MR, Alameldin HF, Awad S,
Boucher E, Caldwell A, Cartwright R,
Charbonneau
A,
Constantinides
B,
Edvenson G, Fay S, Fenton J, Fenzl T,
Fish J, Garcia-Gutierrez L, Garland P,
Gluck J, Gonzalez I, Guermond S, Guo J,
Gupta A, Herr JR, Howe A, Hyer A,
Harpfer A, Irber L, Kidd R, Lin D, Lippi J,
Mansour T, McA’Nulty P, McDonald E,
Mizzi J, Murray KD, Nahum JR, Nanlohy K,
Nederbragt AJ, Ortiz-Zuazaga H, Ory J,
Pell J, Pepe-Ranney C, Russ ZN, Schwarz E,
Scott C, Seaman J, Sievert S, Simpson J, Skennerton CT, Spencer J, Srinivasan R,
Standage D, Stapleton JA, Steinman SR,
Stein J, Taylor B, Trimble W, Wiencko HL,
Wright M, Wyss B, Zhang Q, Zyme E, Brown
CT (2015) The khmer software package:
enabling efficient nucleotide sequence analysis. F1000Res 4:900. https://doi.org/10.
12688/f1000research.6924.1
58. BBNorm Guide. https://jgi.doe.gov/dataand-tools/bbtools/bb-tools-user-guide/
bbnorm-guide/
59. Li H, Handsaker B, Wysoker A, Fennell T,
Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map
format and SAMtools. Bioinformatics 25
(16):2078–2079
60. Van der Auwera GA, Carneiro MO, Hartl C,
Poplin R, Del Angel G, Levy-Moonshine A,
Jordan T, Shakir K, Roazen D, Thibault J,
Banks E, Garimella KV, Altshuler D,
Gabriel S, DePristo MA (2013) From FastQ
data to high confidence variant calls: the
Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11
10 11–11 10 33. https://doi.org/10.1002/
0471250953.bi1110s43
61. Kubica GP, Kim TH, Dunbar FP (1972) Designation of strain H37Rv as the Neotype of
Mycobacterium tuberculosis. Int J Syst Bacteriol 22(2):99–106. https://doi.org/10.1099/
00207713-22-2-99
62. Tindall BJ, Rossello-Mora R, Busse HJ,
Ludwig W, Kampfer P (2010) Notes on the
Mycobacterial ID and Characterization Using WGS
447