116. Walker BJ, Abeel T, Shea T, Priest M,
Abouelliel A, Sakthikumar S, Cuomo CA,
Zeng Q, Wortman J, Young SK (2014)
Pilon: an integrated tool for comprehensive
microbial variant detection and genome
assembly improvement. PLoS One 9(11):
e112963
117. Li H (2018) Minimap2: pairwise alignment
for nucleotide sequences. Bioinformatics 34
(18):3094–3100
118. Wick RR, Schultz MB, Zobel J, Holt KE
(2015) Bandage: interactive visualization of
de novo genome assemblies. Bioinformatics
31(20):3350–3352
119. Brettin T, Davis JJ, Disz T, Edwards RA,
Gerdes S, Olsen GJ, Olson R, Overbeek R,
Parrello B, Pusch GD (2015) RASTtk: a
modular and extensible implementation of
the RAST algorithm for building custom
annotation pipelines and annotating batches
of genomes. Sci Rep 5:8365
120. McNair K, Aziz RK, Pusch GD, Overbeek R,
Dutilh BE, Edwards R (2018) Phage genome
annotation using the RAST pipeline. In: Bacteriophages. Springer, Berlin, pp 231–238
121. Parks DH, Imelfort M, Skennerton CT,
Hugenholtz P, Tyson GW (2015) CheckM:
assessing the quality of microbial genomes
recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055
122. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Cre ´cyLagard V, Diaz N, Disz T, Edwards R (2005)
The subsystems approach to genome annotation and its use in the project to annotate
1000 genomes. Nucleic Acids Res 33
(17):5691–5702
123. Parrello B, Butler R, Chlenski P, Olson R,
Overbeek J, Pusch GD, Vonstein V, Overbeek
R (2019) A machine learning-based service
for estimating quality of genomes using
PATRIC. BMC Bioinformatics 20(1):1–9
124. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch
GD, Shukla M, Vonstein V, Wattam AR, Yoo
H (2016) PATtyFams: protein families for the
microbial genomes in the PATRIC database.
Front Microbiol 7:118
125. Antonopoulos DA, Assaf R, Aziz RK,
Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S (2017) PATRIC
as a unique resource for studying antimicrobial resistance. Brief Bioinform 20
(4):1094–1102
126. Davis JJ, Boisvert S, Brettin T, Kenyon RW,
Mao C, Olson R, Overbeek R, Santerre J,
Shukla M, Wattam AR (2016) Antimicrobial
resistance prediction in PATRIC and RAST.
Sci Rep 6:27930
127. Feldgarden M, Brover V, Haft DH, Prasad
AB, Slotta DJ, Tolstoy I, Tyson GH,
Zhao S, Hsu C-H, McDermott PF (2019)
Validating the AMRFinder tool and resistance
gene database by using antimicrobial resistance genotype-phenotype correlations in a
collection of isolates. Antimicrob Agents
Chemother 63(11):e00483–e00419
128. Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y,
Yang B, Zhang S, Fa Z, Zhao B (2019) Victors: a web-based knowledge base of virulence
factors in human and animal pathogens.
Nucleic Acids Res 47(D1):D693–D700
129. Mao C, Abraham D, Wattam AR, Wilson MJ,
Shukla M, Yoo HS, Sobral BW (2015) Curation, integration and visualization of bacterial
virulence factors in PATRIC. Bioinformatics
31(2):252–258
130. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM
(2016) Mash: fast genome and metagenome
distance estimation using MinHash. Genome
Biol 17(1):132
131. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment
with gene gain, loss and rearrangement.
PLoS One 5(6):e11147
132. Edgar RC (2004) MUSCLE: multiple
sequence alignment with high accuracy and
high throughput. Nucleic Acids Res 32
(5):1792–1797
133. Cock PJ, Antao T, Chang JT, Chapman BA,
Cox CJ, Dalke A, Friedberg I, Hamelryck T,
Kauff F, Wilczynski BJB (2009) Biopython:
freely available Python tools for computational molecular biology and bioinformatics.
Bioinformatics 25(11):1422–1423
134. Stamatakis A (2014) RAxML version 8: a tool
for phylogenetic analysis and post-analysis of
large
phylogenies.
Bioinformatics
30
(9):1312–1313
135. Stamatakis A, Hoover P, Rougemont J (2008)
A rapid bootstrap algorithm for the RAxML
web servers. Syst Biol 57(5):758–771
136. Li H, Durbin R (2009) Fast and accurate
short read alignment with burrows–wheeler
transform.
Bioinformatics
25
(14):1754–1760
137. Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data into alignment
improves DNA read mapping. Nucleic Acids
Res 38(7):e100
138. Garrison E, Marth G (2012) Haplotypebased variant detection from short-read
sequencing. arXiv:1207.3907
139. Aziz RK, Bartels D, Best AA, DeJongh M,
Disz T, Edwards RA, Formsma K, Gerdes S,
Mycobacterial ID and Characterization Using WGS
451
Abouelliel A, Sakthikumar S, Cuomo CA,
Zeng Q, Wortman J, Young SK (2014)
Pilon: an integrated tool for comprehensive
microbial variant detection and genome
assembly improvement. PLoS One 9(11):
e112963
117. Li H (2018) Minimap2: pairwise alignment
for nucleotide sequences. Bioinformatics 34
(18):3094–3100
118. Wick RR, Schultz MB, Zobel J, Holt KE
(2015) Bandage: interactive visualization of
de novo genome assemblies. Bioinformatics
31(20):3350–3352
119. Brettin T, Davis JJ, Disz T, Edwards RA,
Gerdes S, Olsen GJ, Olson R, Overbeek R,
Parrello B, Pusch GD (2015) RASTtk: a
modular and extensible implementation of
the RAST algorithm for building custom
annotation pipelines and annotating batches
of genomes. Sci Rep 5:8365
120. McNair K, Aziz RK, Pusch GD, Overbeek R,
Dutilh BE, Edwards R (2018) Phage genome
annotation using the RAST pipeline. In: Bacteriophages. Springer, Berlin, pp 231–238
121. Parks DH, Imelfort M, Skennerton CT,
Hugenholtz P, Tyson GW (2015) CheckM:
assessing the quality of microbial genomes
recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055
122. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Cre ´cyLagard V, Diaz N, Disz T, Edwards R (2005)
The subsystems approach to genome annotation and its use in the project to annotate
1000 genomes. Nucleic Acids Res 33
(17):5691–5702
123. Parrello B, Butler R, Chlenski P, Olson R,
Overbeek J, Pusch GD, Vonstein V, Overbeek
R (2019) A machine learning-based service
for estimating quality of genomes using
PATRIC. BMC Bioinformatics 20(1):1–9
124. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch
GD, Shukla M, Vonstein V, Wattam AR, Yoo
H (2016) PATtyFams: protein families for the
microbial genomes in the PATRIC database.
Front Microbiol 7:118
125. Antonopoulos DA, Assaf R, Aziz RK,
Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S (2017) PATRIC
as a unique resource for studying antimicrobial resistance. Brief Bioinform 20
(4):1094–1102
126. Davis JJ, Boisvert S, Brettin T, Kenyon RW,
Mao C, Olson R, Overbeek R, Santerre J,
Shukla M, Wattam AR (2016) Antimicrobial
resistance prediction in PATRIC and RAST.
Sci Rep 6:27930
127. Feldgarden M, Brover V, Haft DH, Prasad
AB, Slotta DJ, Tolstoy I, Tyson GH,
Zhao S, Hsu C-H, McDermott PF (2019)
Validating the AMRFinder tool and resistance
gene database by using antimicrobial resistance genotype-phenotype correlations in a
collection of isolates. Antimicrob Agents
Chemother 63(11):e00483–e00419
128. Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y,
Yang B, Zhang S, Fa Z, Zhao B (2019) Victors: a web-based knowledge base of virulence
factors in human and animal pathogens.
Nucleic Acids Res 47(D1):D693–D700
129. Mao C, Abraham D, Wattam AR, Wilson MJ,
Shukla M, Yoo HS, Sobral BW (2015) Curation, integration and visualization of bacterial
virulence factors in PATRIC. Bioinformatics
31(2):252–258
130. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM
(2016) Mash: fast genome and metagenome
distance estimation using MinHash. Genome
Biol 17(1):132
131. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment
with gene gain, loss and rearrangement.
PLoS One 5(6):e11147
132. Edgar RC (2004) MUSCLE: multiple
sequence alignment with high accuracy and
high throughput. Nucleic Acids Res 32
(5):1792–1797
133. Cock PJ, Antao T, Chang JT, Chapman BA,
Cox CJ, Dalke A, Friedberg I, Hamelryck T,
Kauff F, Wilczynski BJB (2009) Biopython:
freely available Python tools for computational molecular biology and bioinformatics.
Bioinformatics 25(11):1422–1423
134. Stamatakis A (2014) RAxML version 8: a tool
for phylogenetic analysis and post-analysis of
large
phylogenies.
Bioinformatics
30
(9):1312–1313
135. Stamatakis A, Hoover P, Rougemont J (2008)
A rapid bootstrap algorithm for the RAxML
web servers. Syst Biol 57(5):758–771
136. Li H, Durbin R (2009) Fast and accurate
short read alignment with burrows–wheeler
transform.
Bioinformatics
25
(14):1754–1760
137. Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data into alignment
improves DNA read mapping. Nucleic Acids
Res 38(7):e100
138. Garrison E, Marth G (2012) Haplotypebased variant detection from short-read
sequencing. arXiv:1207.3907
139. Aziz RK, Bartels D, Best AA, DeJongh M,
Disz T, Edwards RA, Formsma K, Gerdes S,
Mycobacterial ID and Characterization Using WGS
451