species delimitation with confidence intervals
and improved distance functions. BMC bioinformatics 14:60. https://doi.org/10.1186/
1471-2105-14-60
98. Meier-Kolthoff JP, Hahnke RL, Petersen J,
Scheuner C, Michael V, Fiebig A, Rohde C,
Rohde M, Fartmann B, Goodwin LA,
Chertkov O, Reddy T, Pati A, Ivanova NN,
Markowitz V, Kyrpides NC, Woyke T,
Go ¨ker M, Klenk HP (2014) Complete
genome sequence of DSM 30083
T
, the type
strain (U5/41
T ) of Escherichia coli, and a proposal for delineating subspecies in microbial
taxonomy. Stand Genomic Sci 9:2. https://
doi.org/10.1186/1944-3277-9-2
99. Stackebrandt E, Frederiksen W, Garrity GM,
Grimont PA, Kampfer P, Maiden MC,
Nesme X, Rossello-Mora R, Swings J, Truper
HG, Vauterin L, Ward AC, Whitman WB
(2002) Report of the ad hoc committee for
the re-evaluation of the species definition in
bacteriology. Int J Syst Evol Microbiol 52
(Pt 3):1043–1047. https://doi.org/10.
1099/00207713-52-3-1043
100. Rossello-Mora R (2012) Towards a taxonomy
of Bacteria and Archaea based on interactive
and cumulative data repositories. Environ
Microbiol 14(2):318–334. https://doi.org/
10.1111/j.1462-2920.2011.02599.x
101. Sutcliffe IC, Trujillo ME, Goodfellow M
(2012) A call to arms for systematists: revitalising the purpose and practises underpinning
the description of novel microbial taxa. Antonie Van Leeuwenhoek 101(1):13–20.
https://doi.org/10.1007/s10482-0119664-0
102. Thompson CC, Amaral GR, Campeao M,
Edwards RA, Polz MF, Dutilh BE, Ussery
DW, Sawabe T, Swings J, Thompson FL
(2015) Microbial taxonomy in the postgenomic era: rebuilding from scratch? Arch
Microbiol 197(3):359–370. https://doi.
org/10.1007/s00203-014-1071-2
103. Parker CT, Tindall BJ, Garrity GM (2019)
International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69(1A):
S1–S111. https://doi.org/10.1099/ijsem.0.
000778
104. Tagini F, Aeby S, Bertelli C, Droz S,
Casanova C, Prod’hom G, Jaton K, Greub G
(2019) Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level
lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens
sp. nov. and Mycobacterium attenuatum
sp. nov. Int J Syst Evol Microbiol 69
(6):1696–1704. https://doi.org/10.1099/
ijsem.0.003378
105. Davis JJ, Wattam AR, Aziz RK, Brettin T,
Butler R, Butler RM, Chlenski P, Conrad N,
Dickerman A, Dietrich EM (2020) The
PATRIC bioinformatics resource center:
expanding data and analysis capabilities.
Nucleic Acids Res 48(D1):D606–D612
106. Wattam AR, Abraham D, Dalay O, Disz TL,
Driscoll T, Gabbard JL, Gillespie JJ,
Gough R, Hix D, Kenyon R (2013) PATRIC,
the bacterial bioinformatics database and
analysis resource. Nucleic Acids Res 42(D1):
D581–D591
107. Wattam AR, Davis JJ, Assaf R, Boisvert S,
Brettin T, Bun C, Conrad N, Dietrich EM,
Disz T, Gabbard JL (2016) Improvements to
PATRIC, the all-bacterial bioinformatics
database and analysis resource center. Nucleic
Acids Res 45(D1):D535–D542
108. Krueger F (2012) Trim Galore! A wrapper
tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to
FastQ files, with some extra functionality for
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. http://www.
bioinformatics.babraham.ac.uk/projects/
trim_galore/. Accessed 28 04 2016
109. Lassmann T, Hayashizaki Y, Daub CO (2010)
SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27
(1):130–131
110. Ondov BD, Bergman NH, Phillippy AM
(2011) Interactive metagenomic visualization
in a web browser. BMC Bioinformatics 12
(1):385
111. Clausen PT, Aarestrup FM, Lund O (2018)
Rapid and precise alignment of raw reads
against redundant databases with KMA.
BMC Bioinformatics 19(1):307
112. McArthur AG, Waglechner N, Nizam F,
Yan A, Azad MA, Baylay AJ, Bhullar K,
Canova MJ, De Pascale G, Ejim L (2013)
The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57
(7):3348–3357
113. Chen L, Xiong Z, Sun L, Yang J, Jin Q (2011)
VFDB 2012 update: toward the genetic
diversity and molecular evolution of bacterial
virulence factors. Nucleic Acids Res 40(D1):
D641–D645
114. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile
metagenomic assembler. Genome Res 27
(5):824–834
115. Antipov D, Hartwick N, Shen M, Raiko M,
Lapidus A, Pevzner P (2016) plasmidSPAdes:
assembling plasmids from whole genome
sequencing data. bioRxiv:048942
450
Marco A. Riojas et al.
and improved distance functions. BMC bioinformatics 14:60. https://doi.org/10.1186/
1471-2105-14-60
98. Meier-Kolthoff JP, Hahnke RL, Petersen J,
Scheuner C, Michael V, Fiebig A, Rohde C,
Rohde M, Fartmann B, Goodwin LA,
Chertkov O, Reddy T, Pati A, Ivanova NN,
Markowitz V, Kyrpides NC, Woyke T,
Go ¨ker M, Klenk HP (2014) Complete
genome sequence of DSM 30083
T
, the type
strain (U5/41
T ) of Escherichia coli, and a proposal for delineating subspecies in microbial
taxonomy. Stand Genomic Sci 9:2. https://
doi.org/10.1186/1944-3277-9-2
99. Stackebrandt E, Frederiksen W, Garrity GM,
Grimont PA, Kampfer P, Maiden MC,
Nesme X, Rossello-Mora R, Swings J, Truper
HG, Vauterin L, Ward AC, Whitman WB
(2002) Report of the ad hoc committee for
the re-evaluation of the species definition in
bacteriology. Int J Syst Evol Microbiol 52
(Pt 3):1043–1047. https://doi.org/10.
1099/00207713-52-3-1043
100. Rossello-Mora R (2012) Towards a taxonomy
of Bacteria and Archaea based on interactive
and cumulative data repositories. Environ
Microbiol 14(2):318–334. https://doi.org/
10.1111/j.1462-2920.2011.02599.x
101. Sutcliffe IC, Trujillo ME, Goodfellow M
(2012) A call to arms for systematists: revitalising the purpose and practises underpinning
the description of novel microbial taxa. Antonie Van Leeuwenhoek 101(1):13–20.
https://doi.org/10.1007/s10482-0119664-0
102. Thompson CC, Amaral GR, Campeao M,
Edwards RA, Polz MF, Dutilh BE, Ussery
DW, Sawabe T, Swings J, Thompson FL
(2015) Microbial taxonomy in the postgenomic era: rebuilding from scratch? Arch
Microbiol 197(3):359–370. https://doi.
org/10.1007/s00203-014-1071-2
103. Parker CT, Tindall BJ, Garrity GM (2019)
International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69(1A):
S1–S111. https://doi.org/10.1099/ijsem.0.
000778
104. Tagini F, Aeby S, Bertelli C, Droz S,
Casanova C, Prod’hom G, Jaton K, Greub G
(2019) Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level
lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens
sp. nov. and Mycobacterium attenuatum
sp. nov. Int J Syst Evol Microbiol 69
(6):1696–1704. https://doi.org/10.1099/
ijsem.0.003378
105. Davis JJ, Wattam AR, Aziz RK, Brettin T,
Butler R, Butler RM, Chlenski P, Conrad N,
Dickerman A, Dietrich EM (2020) The
PATRIC bioinformatics resource center:
expanding data and analysis capabilities.
Nucleic Acids Res 48(D1):D606–D612
106. Wattam AR, Abraham D, Dalay O, Disz TL,
Driscoll T, Gabbard JL, Gillespie JJ,
Gough R, Hix D, Kenyon R (2013) PATRIC,
the bacterial bioinformatics database and
analysis resource. Nucleic Acids Res 42(D1):
D581–D591
107. Wattam AR, Davis JJ, Assaf R, Boisvert S,
Brettin T, Bun C, Conrad N, Dietrich EM,
Disz T, Gabbard JL (2016) Improvements to
PATRIC, the all-bacterial bioinformatics
database and analysis resource center. Nucleic
Acids Res 45(D1):D535–D542
108. Krueger F (2012) Trim Galore! A wrapper
tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to
FastQ files, with some extra functionality for
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. http://www.
bioinformatics.babraham.ac.uk/projects/
trim_galore/. Accessed 28 04 2016
109. Lassmann T, Hayashizaki Y, Daub CO (2010)
SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27
(1):130–131
110. Ondov BD, Bergman NH, Phillippy AM
(2011) Interactive metagenomic visualization
in a web browser. BMC Bioinformatics 12
(1):385
111. Clausen PT, Aarestrup FM, Lund O (2018)
Rapid and precise alignment of raw reads
against redundant databases with KMA.
BMC Bioinformatics 19(1):307
112. McArthur AG, Waglechner N, Nizam F,
Yan A, Azad MA, Baylay AJ, Bhullar K,
Canova MJ, De Pascale G, Ejim L (2013)
The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57
(7):3348–3357
113. Chen L, Xiong Z, Sun L, Yang J, Jin Q (2011)
VFDB 2012 update: toward the genetic
diversity and molecular evolution of bacterial
virulence factors. Nucleic Acids Res 40(D1):
D641–D645
114. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile
metagenomic assembler. Genome Res 27
(5):824–834
115. Antipov D, Hartwick N, Shen M, Raiko M,
Lapidus A, Pevzner P (2016) plasmidSPAdes:
assembling plasmids from whole genome
sequencing data. bioRxiv:048942
450
Marco A. Riojas et al.