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1472-765X.2008.02372.x
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efficient, and safe method to prepare high
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1016/j.jctube.2020.100150
29. Hasan NA, Epperson LE, Lawsin A, Rodger
RR, Perkins KM, Halpin AL, Perry KA,
Moulton-Meissner H, Diekema DJ, Crist
MB, Perz JF, Salfinger M, Daley CL, Strong
M (2019) Genomic analysis of cardiac
surgery-associated Mycobacterium chimaera
infections, United States. Emerg Infect Dis
25(3):559–563. https://doi.org/10.3201/
eid2503.181282
30. Andrews S (2010) FastQC: a quality control
tool for high throughput sequence data.
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uk/projects/fastqc/
31. De Coster W, D’Hert S, Schultz DT,
Cruts M, Van Broeckhoven C (2018) NanoPack: visualizing and processing long-read
sequencing
data.
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34
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bioinformatics/bty149
32. Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp:
an ultra-fast all-in-one FASTQ preprocessor.
Bioinformatics 34(17):i884–i890. https://
doi.org/10.1093/bioinformatics/bty560
33. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina
sequence
data.
Bioinformatics
30
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bioinformatics/btu170
34. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
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14806/ej.17.1.200
35. Wick RR Filtlong. https://github.com/
rrwick/Filtlong
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on Multiplexing and Downstream Analysis.
vol 770–2017–004-D
37. Wick RR, Judd LM, Holt KE (2018) Deepbinner: Demultiplexing barcoded Oxford
Nanopore reads with deep convolutional neural networks. PLoS Comput Biol 14(11):
e1006583. https://doi.org/10.1371/jour
nal.pcbi.1006583
38. Wood DE, Lu J, Langmead B (2019)
Improved metagenomic analysis with kraken
2. Genome Biol 20(1):257. https://doi.org/
10.1186/s13059-019-1891-0
39. Langmead B, Salzberg SL (2012) Fast
gapped-read alignment with bowtie 2. Nat
Methods 9(4):357–359. https://doi.org/10.
1038/nmeth.1923
40. Li H (2013) Aligning sequence reads, clone
sequences and assembly contigs with
BWA-MEM. arXiv:1303.3997
41. Zerbino DR (2010) Using the velvet de novo
assembler for short-read sequencing technologies.
Curr
Protoc
Bioinformatics.
Chapter 11:Unit 11 15. https://doi.org/10.
1002/0471250953.bi1105s31
42. Jackman SD, Vandervalk BP, Mohamadi H,
Chu J, Yeo S, Hammond SA, Jahesh G,
Khan H, Coombe L, Warren RL, Birol I
446
Marco A. Riojas et al.
DNA sequencing with chain-terminating
inhibitors. Proc Natl Acad Sci U S A 74
(12):5463–5467. https://doi.org/10.1073/
pnas.74.12.5463
19. Heather JM, Chain B (2016) The sequence of
sequencers: the history of sequencing DNA.
Genomics 107(1):1–8. https://doi.org/10.
1016/j.ygeno.2015.11.003
20. Goodwin S, McPherson JD, McCombie WR
(2016) Coming of age: ten years of nextgeneration sequencing technologies. Nat
Rev Genet 17(6):333–351. https://doi.org/
10.1038/nrg.2016.49
21. Illumina, Inc. (2010) Technology Spotlight:
Illumina® Sequencing
22. Giani AM, Gallo GR, Gianfranceschi L, Formenti G (2020) Long walk to genomics: history and current approaches to genome
sequencing and assembly. Comput Struct Biotechnol J 18:9–19. https://doi.org/10.
1016/j.csbj.2019.11.002
23. Pacific Biosciences of California, Inc. SMRT
Sequencing—How
it
Works.
vol
PS100–032919
24. McCombie WR, McPherson JD, Mardis ER
(2019) Next-generation sequencing technologies. Cold Spring Harb Perspect Med 9(11).
https://doi.org/10.1101/cshperspect.
a036798
25. Marrakchi H, Laneelle MA, Daffe M (2014)
Mycolic acids: structures, biosynthesis, and
beyond. Chem Biol 21(1):67–85. https://
doi.org/10.1016/j.chembiol.2013.11.011
26. Jackson M (2014) The mycobacterial cell
envelope-lipids. Cold Spring Harb Perspect
Med
4(10).
https://doi.org/10.1101/
cshperspect.a021105
27. Amaro A, Duarte E, Amado A, Ferronha H,
Botelho A (2008) Comparison of three DNA
extraction methods for Mycobacterium bovis,
Mycobacterium tuberculosis and Mycobacterium avium subsp. avium. Lett Appl Microbiol 47(1):8–11. https://doi.org/10.1111/j.
1472-765X.2008.02372.x
28. Epperson LE, Strong M (2020) A scalable,
efficient, and safe method to prepare high
quality DNA from mycobacteria and other
challenging cells. J Clin Tuberc Other Mycobact Dis 19:100150. https://doi.org/10.
1016/j.jctube.2020.100150
29. Hasan NA, Epperson LE, Lawsin A, Rodger
RR, Perkins KM, Halpin AL, Perry KA,
Moulton-Meissner H, Diekema DJ, Crist
MB, Perz JF, Salfinger M, Daley CL, Strong
M (2019) Genomic analysis of cardiac
surgery-associated Mycobacterium chimaera
infections, United States. Emerg Infect Dis
25(3):559–563. https://doi.org/10.3201/
eid2503.181282
30. Andrews S (2010) FastQC: a quality control
tool for high throughput sequence data.
https://www.bioinformatics.babraham.ac.
uk/projects/fastqc/
31. De Coster W, D’Hert S, Schultz DT,
Cruts M, Van Broeckhoven C (2018) NanoPack: visualizing and processing long-read
sequencing
data.
Bioinformatics
34
(15):2666–2669. https://doi.org/10.1093/
bioinformatics/bty149
32. Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp:
an ultra-fast all-in-one FASTQ preprocessor.
Bioinformatics 34(17):i884–i890. https://
doi.org/10.1093/bioinformatics/bty560
33. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina
sequence
data.
Bioinformatics
30
(15):2114–2120. https://doi.org/10.1093/
bioinformatics/btu170
34. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
reads. EMBnetJ 17(1). https://doi.org/10.
14806/ej.17.1.200
35. Wick RR Filtlong. https://github.com/
rrwick/Filtlong
36. Illumina, Inc. Effects of Index Misassignment
on Multiplexing and Downstream Analysis.
vol 770–2017–004-D
37. Wick RR, Judd LM, Holt KE (2018) Deepbinner: Demultiplexing barcoded Oxford
Nanopore reads with deep convolutional neural networks. PLoS Comput Biol 14(11):
e1006583. https://doi.org/10.1371/jour
nal.pcbi.1006583
38. Wood DE, Lu J, Langmead B (2019)
Improved metagenomic analysis with kraken
2. Genome Biol 20(1):257. https://doi.org/
10.1186/s13059-019-1891-0
39. Langmead B, Salzberg SL (2012) Fast
gapped-read alignment with bowtie 2. Nat
Methods 9(4):357–359. https://doi.org/10.
1038/nmeth.1923
40. Li H (2013) Aligning sequence reads, clone
sequences and assembly contigs with
BWA-MEM. arXiv:1303.3997
41. Zerbino DR (2010) Using the velvet de novo
assembler for short-read sequencing technologies.
Curr
Protoc
Bioinformatics.
Chapter 11:Unit 11 15. https://doi.org/10.
1002/0471250953.bi1105s31
42. Jackman SD, Vandervalk BP, Mohamadi H,
Chu J, Yeo S, Hammond SA, Jahesh G,
Khan H, Coombe L, Warren RL, Birol I
446
Marco A. Riojas et al.