Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
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C Chewapreecha, 2014, Dense genomic sampling identifies highways of pneumococcal recombination, Nat Genet, 46, 305, 10.1038/ng.2895
I Comas, 2013, Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nat Genet, 45, 1176, 10.1038/ng.2744
NJ Croucher, 2013, Population genomics of post-vaccine changes in pneumococcal epidemiology, Nat Genet, 45, 656, 10.1038/ng.2625
YH Grad, 2014, Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study, Lancet Infect Dis, 14, 220, 10.1016/S1473-3099(13)70693-5
R Ronen, 2012, SEQuel: improving the accuracy of genome assemblies, Bioinformatics, 28, i188, 10.1093/bioinformatics/bts219
MT Swain, 2012, A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs, Nat Protoc, 7, 1260, 10.1038/nprot.2012.068
M Hunt, 2013, REAPR: a universal tool for genome assembly evaluation, Genome Biol, 14, R47, 10.1186/gb-2013-14-5-r47
R Vicedomini, 2013, GAM-NGS: genomic assemblies merger for next generation sequencing, BMC Bioinformatics, 14, S6, 10.1186/1471-2105-14-S7-S6
H Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
A McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, 20, 1297, 10.1101/gr.107524.110
S Pabinger, 2013, A survey of tools for variant analysis of next-generation genome sequencing data, Brief Bioinform, 15, 256, 10.1093/bib/bbs086
A Cubillos-Ruiz, 2008, Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments, BMC Res Notes, 1, 110, 10.1186/1756-0500-1-110
S El-Metwally, 2013, Next-generation sequence assembly: four stages of data processing and computational challenges, PLoS Comput Biol, 9, e1003345, 10.1371/journal.pcbi.1003345
H Tettelin, 2001, Complete genome sequence of a virulent isolate of Streptococcus pneumoniae, Science, 293, 498, 10.1126/science.1061217
H Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
IJ Tsai, 2010, Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps, Genome Biol, 11, R41, 10.1186/gb-2010-11-4-r41
F Nadalin, 2012, GapFiller: a de novo assembly approach to fill the gap within paired reads, BMC Bioinformatics, 13, S8, 10.1186/1471-2105-13-S14-S8
TD Otto, 2010, Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology, Bioinformatics, 26, 1704, 10.1093/bioinformatics/btq269
R Luo, 2005, Solution structure of choline binding protein A, the major adhesin of Streptococcus pneumoniae, EMBO J, 24, 34, 10.1038/sj.emboj.7600490
AH Tu, 1999, Pneumococcal surface protein A inhibits complement activation by Streptococcus pneumoniae, Infect Immun, 67, 4720, 10.1128/IAI.67.9.4720-4724.1999
G Butler, 2009, Evolution of pathogenicity and sexual reproduction in eight Candida genomes, Nature, 459, 657, 10.1038/nature08064
T Jones, 2004, The diploid genome sequence of Candida albicans, Proc Natl Acad Sci U S A, 101, 7329, 10.1073/pnas.0401648101
D Muzzey, 2013, Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure, Genome Biol, 14, R97, 10.1186/gb-2013-14-9-r97
K Chen, 2009, BreakDancer: an algorithm for high-resolution mapping of genomic structural variation, Nat Methods, 6, 677, 10.1038/nmeth.1363
T Marschall, 2012, CLEVER: clique-enumerating variant finder, Bioinformatics, 28, 2875, 10.1093/bioinformatics/bts566
B Weiner, 2012, Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region, PLoS One, 7, e26038, 10.1371/journal.pone.0026038
TR Ioerger, 2010, Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories, J Bacteriol, 192, 3645, 10.1128/JB.00166-10
S Kohli, 2012, Comparative genomic and proteomic analyses of PE/PPE multigene family of Mycobacterium tuberculosis H<sub>37</sub>Rv and H<sub>37</sub>Ra reveal novel and interesting differences with implications in virulence, Nucleic Acids Res, 40, 7113, 10.1093/nar/gks465
HM Vordermeier, 2012, Conserved immune recognition hierarchy of mycobacterial PE/PPE proteins during infection in natural hosts, PLoS One, 7, e40890, 10.1371/journal.pone.0040890
S Das, 1995, IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, south India, Tuber Lung Dis, 76, 550, 10.1016/0962-8479(95)90533-2
A Karboul, 2008, Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: potential role in antigenic variability, J Bacteriol, 190, 7838, 10.1128/JB.00827-08
C Ford, 2012, Mycobacterium tuberculosis—heterogeneity revealed through whole genome sequencing, Tuberculosis (Edinb), 92, 194, 10.1016/j.tube.2011.11.003
CRE McEvoy, 2012, Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints, PLoS One, 7, e30593, 10.1371/journal.pone.0030593
H Thorvaldsdóttir, 2013, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, 14, 178, 10.1093/bib/bbs017
T Abeel, 2012, GenomeView: a next-generation genome browser, Nucleic Acids Res, 40, e12, 10.1093/nar/gkr995
MG Ross, 2013, Characterizing and measuring bias in sequence data, Genome Biol, 14, R51, 10.1186/gb-2013-14-5-r51
YH Grad, 2012, Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011, Proc Natl Acad Sci U S A, 109, 3065, 10.1073/pnas.1121491109
FJ Ribeiro, 2012, Finished bacterial genomes from shotgun sequence data, Genome Res, 22, 2270, 10.1101/gr.141515.112
LJS Williams, 2012, Paired-end sequencing of Fosmid libraries by Illumina, Genome Res, 22, 2241, 10.1101/gr.138925.112
S Gnerre, 2011, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proc Natl Acad Sci U S A, 108, 1513, 10.1073/pnas.1017351108
SF Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
AL Delcher, 2002, Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Res, 30, 2478, 10.1093/nar/30.11.2478
a Larkin M, 2007, Clustal W and Clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404
TA Tatusova, 1999, BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences, FEMS Microbiol Lett, 174, 247, 10.1111/j.1574-6968.1999.tb13575.x