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| 2 | + author = {Stephens, Z. D. and Hudson, M. E. and Mainzer, L. S. and Taschuk, M. and Weber, M. R. and Iyer, R. K.}, |
| 3 | + title = {Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models}, |
| 4 | + journal = {PLOS ONE}, |
| 5 | + year = {2016}, |
| 6 | + volume = {11}, |
| 7 | + number = {11}, |
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| 9 | + doi = {10.1371/journal.pone.0167047} |
| 10 | +} |
| 11 | + |
| 12 | +@article{Benjamini:2012, |
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| 14 | + title = {Summarizing and correcting the {GC} content bias in high-throughput sequencing}, |
| 15 | + journal = {Nucleic Acids Research}, |
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| 21 | +} |
| 22 | + |
| 23 | +@article{Ross:2013, |
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| 25 | + title = {Characterizing and measuring bias in sequence data}, |
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| 32 | +} |
| 33 | + |
| 34 | +@article{Escalona:2016, |
| 35 | + author = {Escalona, M. and Rocha, S. and Posada, D.}, |
| 36 | + title = {A comparison of tools for the simulation of genomic next-generation sequencing data}, |
| 37 | + journal = {Nature Reviews Genetics}, |
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| 43 | +} |
| 44 | + |
| 45 | +@article{Zhao:2017, |
| 46 | + author = {Zhao, M. and Liu, D. and Qu, H.}, |
| 47 | + title = {Systematic review of next-generation sequencing simulators: computational tools, features and perspectives}, |
| 48 | + journal = {Briefings in Functional Genomics}, |
| 49 | + year = {2017}, |
| 50 | + volume = {16}, |
| 51 | + number = {3}, |
| 52 | + pages = {121--128}, |
| 53 | + doi = {10.1093/bfgp/elw012} |
| 54 | +} |
| 55 | + |
| 56 | +@article{Alosaimi:2020, |
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| 58 | + title = {A broad survey of {DNA} sequence data simulation tools}, |
| 59 | + journal = {Briefings in Functional Genomics}, |
| 60 | + year = {2020}, |
| 61 | + volume = {19}, |
| 62 | + number = {1}, |
| 63 | + pages = {49--59}, |
| 64 | + doi = {10.1093/bfgp/elz033} |
| 65 | +} |
| 66 | + |
| 67 | +@article{Milhaven:2023, |
| 68 | + author = {Milhaven, M. and Pfeifer, S. P.}, |
| 69 | + title = {Performance evaluation of six popular short-read simulators}, |
| 70 | + journal = {Heredity}, |
| 71 | + year = {2023}, |
| 72 | + volume = {130}, |
| 73 | + pages = {55--63}, |
| 74 | + doi = {10.1038/s41437-022-00577-3} |
| 75 | +} |
| 76 | + |
| 77 | +@article{Schmeing:2021, |
| 78 | + author = {Schmeing, S. and Robinson, M. D.}, |
| 79 | + title = {{ReSeq} simulates realistic {Illumina} high-throughput sequencing data}, |
| 80 | + journal = {Genome Biology}, |
| 81 | + year = {2021}, |
| 82 | + volume = {22}, |
| 83 | + pages = {67}, |
| 84 | + doi = {10.1186/s13059-021-02265-7} |
| 85 | +} |
| 86 | + |
| 87 | +@article{Huang:2012, |
| 88 | + author = {Huang, W. and Li, L. and Myers, J. R. and Marth, G. T.}, |
| 89 | + title = {{ART}: a next-generation sequencing read simulator}, |
| 90 | + journal = {Bioinformatics}, |
| 91 | + year = {2012}, |
| 92 | + volume = {28}, |
| 93 | + number = {4}, |
| 94 | + pages = {593--594}, |
| 95 | + doi = {10.1093/bioinformatics/btr708} |
| 96 | +} |
| 97 | + |
| 98 | +@article{Caboche:2014, |
| 99 | + author = {Caboche, S. and Audebert, C. and Lemoine, Y. and Hot, D.}, |
| 100 | + title = {Comparison of mapping algorithms used in high-throughput sequencing: application to {Ion Torrent} data}, |
| 101 | + journal = {BMC Genomics}, |
| 102 | + year = {2014}, |
| 103 | + volume = {15}, |
| 104 | + pages = {264}, |
| 105 | + doi = {10.1186/1471-2164-15-264} |
| 106 | +} |
| 107 | + |
| 108 | +@misc{Homer:2010, |
| 109 | + author = {Homer, N.}, |
| 110 | + title = {{DWGSIM}: Whole Genome Simulator for Next-Generation Sequencing}, |
| 111 | + year = {2010}, |
| 112 | + howpublished = {GitHub repository}, |
| 113 | + url = {https://github.com/nh13/DWGSIM} |
| 114 | +} |
| 115 | + |
| 116 | +@article{McElroy:2012, |
| 117 | + author = {McElroy, K. E. and Luciani, F. and Thomas, T.}, |
| 118 | + title = {{GemSIM}: general, error-model based simulator of next-generation sequencing data}, |
| 119 | + journal = {BMC Genomics}, |
| 120 | + year = {2012}, |
| 121 | + volume = {13}, |
| 122 | + pages = {74}, |
| 123 | + doi = {10.1186/1471-2164-13-74} |
| 124 | +} |
| 125 | + |
| 126 | +@article{Gourle:2019, |
| 127 | + author = {Gourl{\'e}, H. and Karlsson-Lindsj{\"o}, O. and Hayer, J. and Bongcam-Rudloff, E.}, |
| 128 | + title = {Simulating {Illumina} metagenomic data with {InSilicoSeq}}, |
| 129 | + journal = {Bioinformatics}, |
| 130 | + year = {2019}, |
| 131 | + volume = {35}, |
| 132 | + number = {3}, |
| 133 | + pages = {521--522}, |
| 134 | + doi = {10.1093/bioinformatics/bty630} |
| 135 | +} |
| 136 | + |
| 137 | +@misc{Holtgrewe:2010, |
| 138 | + author = {Holtgrewe, M.}, |
| 139 | + title = {Mason -- {A} Read Simulator for Second Generation Sequencing Data}, |
| 140 | + year = {2010}, |
| 141 | + howpublished = {Technical Report TR-B-10-06}, |
| 142 | + institution = {Freie Universit{\"a}t Berlin, Fachbereich Mathematik und Informatik}, |
| 143 | + number = {B-10-06}, |
| 144 | + url = {https://publications.imp.fu-berlin.de/962/2/mason201009.pdf} |
| 145 | +} |
| 146 | + |
| 147 | +@article{Hu:2012, |
| 148 | + author = {Hu, Xuesong and Yuan, Jianying and Shi, Yujian and Lu, Jianliang and Liu, Binghang and Li, Zhenyu and Chen, Yanxiang and Mu, Desheng and Zhang, Hao and Li, Nan and Yue, Zhen and Bai, Fan and Li, Heng and Fan, Wei}, |
| 149 | + title = {{pIRS}: Profile-based {Illumina} paired-end reads simulator}, |
| 150 | + journal = {Bioinformatics}, |
| 151 | + year = {2012}, |
| 152 | + volume = {28}, |
| 153 | + number = {11}, |
| 154 | + pages = {1533--1535}, |
| 155 | + doi = {10.1093/bioinformatics/bts187} |
| 156 | +} |
| 157 | + |
| 158 | +@article{Pattnaik:2014, |
| 159 | + author = {Pattnaik, S. and Gupta, S. and Rao, A. A. and Panda, B.}, |
| 160 | + title = {{SInC}: an accurate and fast error-model based simulator for {SNPs}, {Indels} and {CNVs} coupled with a read generator for short-read sequence data}, |
| 161 | + journal = {BMC Bioinformatics}, |
| 162 | + year = {2014}, |
| 163 | + volume = {15}, |
| 164 | + pages = {40}, |
| 165 | + doi = {10.1186/1471-2105-15-40} |
| 166 | +} |
| 167 | + |
| 168 | +@misc{Li:2011, |
| 169 | + author = {Li, Heng}, |
| 170 | + title = {{wgsim}-{Read} simulator for next generation sequencing}, |
| 171 | + year = {2011}, |
| 172 | + howpublished = {GitHub repository}, |
| 173 | + url = {https://github.com/lh3/wgsim} |
| 174 | +} |
| 175 | + |
| 176 | +@article{Rhie:2023, |
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| 178 | + title = {The complete sequence of a human {Y} chromosome}, |
| 179 | + journal = {Nature}, |
| 180 | + year = {2023}, |
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| 182 | + number = {7978}, |
| 183 | + pages = {344--354}, |
| 184 | + doi = {10.1038/s41586-023-06457-y} |
| 185 | +} |
| 186 | + |
| 187 | +@article{Lefouili:2022, |
| 188 | + author = {Lefouili, M. and Nam, K.}, |
| 189 | + title = {The evaluation of {Bcftools} mpileup and {GATK} {HaplotypeCaller} for variant calling in non-human species}, |
| 190 | + journal = {Scientific Reports}, |
| 191 | + year = {2022}, |
| 192 | + volume = {12}, |
| 193 | + pages = {11331}, |
| 194 | + doi = {10.1038/s41598-022-15563-2} |
| 195 | +} |
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| 197 | +@article{Zhao:2020, |
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| 199 | + title = {Accuracy and efficiency of germline variant calling pipelines for human genome data}, |
| 200 | + journal = {Scientific Reports}, |
| 201 | + year = {2020}, |
| 202 | + volume = {10}, |
| 203 | + pages = {20222}, |
| 204 | + doi = {10.1038/s41598-020-77218-4} |
| 205 | +} |
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| 207 | +@article{Ahmed:2019, |
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| 209 | + title = {Managing genomic variant calling workflows with {Swift/T}}, |
| 210 | + journal = {PLOS ONE}, |
| 211 | + year = {2019}, |
| 212 | + volume = {14}, |
| 213 | + number = {7}, |
| 214 | + pages = {e0211608}, |
| 215 | + doi = {10.1371/journal.pone.0211608} |
| 216 | +} |
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| 218 | +@article{Kendig:2019, |
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| 220 | + title = {Sentieon {DNASeq} Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy}, |
| 221 | + journal = {Frontiers in Genetics}, |
| 222 | + year = {2019}, |
| 223 | + volume = {10}, |
| 224 | + pages = {736}, |
| 225 | + doi = {10.3389/fgene.2019.00736} |
| 226 | +} |
| 227 | + |
| 228 | +@article{RuizSchultz:2021, |
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| 230 | + title = {Methods and feasibility study for exome sequencing as a universal second-tier test in newborn screening}, |
| 231 | + journal = {Genetics in Medicine}, |
| 232 | + year = {2021}, |
| 233 | + volume = {23}, |
| 234 | + number = {4}, |
| 235 | + pages = {767--776}, |
| 236 | + doi = {10.1038/s41436-020-01058-w} |
| 237 | +} |
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| 241 | + title = {Computational pan-genome mapping and pairwise {SNP}-distance improve detection of {\textit{Mycobacterium tuberculosis}} transmission clusters}, |
| 242 | + journal = {PLOS Computational Biology}, |
| 243 | + year = {2019}, |
| 244 | + volume = {15}, |
| 245 | + number = {12}, |
| 246 | + pages = {e1007527}, |
| 247 | + doi = {10.1371/journal.pcbi.1007527} |
| 248 | +} |
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| 250 | +@article{Shah:2021, |
| 251 | + author = {Shah, R. N. and Ruthenburg, A. J.}, |
| 252 | + title = {Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads}, |
| 253 | + journal = {PLOS Computational Biology}, |
| 254 | + year = {2021}, |
| 255 | + volume = {17}, |
| 256 | + number = {4}, |
| 257 | + pages = {e1008926}, |
| 258 | + doi = {10.1371/journal.pcbi.1008926} |
| 259 | +} |
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| 261 | +@article{Delhomme:2020, |
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| 263 | + title = {Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data}, |
| 264 | + journal = {NAR Genomics and Bioinformatics}, |
| 265 | + year = {2020}, |
| 266 | + volume = {2}, |
| 267 | + number = {2}, |
| 268 | + pages = {lqaa021}, |
| 269 | + doi = {10.1093/nargab/lqaa021} |
| 270 | +} |
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