Daetwyler, H. D. et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genet.46, 858–865 (2014). CASPubMed Google Scholar
The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature447, 661–678 (2007).
Sheridan, C. Illumina claims $1,000 genome win. Nature Biotech.32, 115 (2014). Google Scholar
Futschik, A. & Schlötterer, C. The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics186, 207–218 (2010). This study is the first to provide a statistical framework for the analysis of Pool-seq data in population genetics. CASPubMedPubMed Central Google Scholar
Gautier, M. et al. Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping. Mol. Ecol.22, 3766–3779 (2013). CASPubMed Google Scholar
Bamshad, M. J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nature Rev. Genet.12, 745–755 (2011). CASPubMed Google Scholar
Gilissen, C., Hoischen, A., Brunner, H. G. & Veltman, J. A. Disease gene identification strategies for exome sequencing. Eur. J. Hum. Genet.20, 490–497 (2012). CASPubMedPubMed Central Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-seq: a revolutionary tool for transcriptomics. Nature Rev. Genet.10, 57–63 (2009). CASPubMed Google Scholar
Davey, J. W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Rev. Genet.12, 499–510 (2011). CASPubMed Google Scholar
Pihlstrom, L., Rengmark, A., Bjornara, K. A. & Toft, M. Effective variant detection by targeted deep sequencing of DNA pools: an example from Parkinson's disease. Ann. Hum. Genet.78, 243–252 (2014). CASPubMed Google Scholar
Suvorov, A. et al. Intra-specific regulatory variation in Drosophila pseudoobscura. PLoS ONE8, e83547 (2013). PubMedPubMed Central Google Scholar
Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Regulatory changes underlying expression differences within and between Drosophila species. Nature Genet.40, 346–350 (2008). CASPubMed Google Scholar
Konczal, M., Koteja, P., Stuglik, M. T., Radwan, J. & Babik, W. Accuracy of allele frequency estimation using pooled RNA-seq. Mol. Ecol. Resour.14, 381–392 (2014). CASPubMed Google Scholar
Gross, J. B., Furterer, A., Carlson, B. M. & Stahl, B. A. An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus. PLoS ONE8, e55659 (2013). CASPubMedPubMed Central Google Scholar
Kozak, G. M., Brennan, R. S., Berdan, E. L., Fuller, R. C. & Whitehead, A. Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches. Evolution68, 63–80 (2014). CASPubMed Google Scholar
Sloan, D. B. et al. De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Mol. Ecol. Resour.12, 333–343 (2012). CASPubMed Google Scholar
Gautier, M. et al. The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Mol. Ecol.22, 3165–3178 (2013). CASPubMed Google Scholar
Arnold, B., Corbett-Detig, R. B., Hartl, D. & Bomblies, K. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol. Ecol.22, 3179–3190 (2013). CASPubMed Google Scholar
Karczewski, K. J. et al. Systematic functional regulatory assessment of disease-associated variants. Proc. Natl Acad. Sci. USA110, 9607–9612 (2013). CASPubMedPubMed Central Google Scholar
Khurana, E. et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science342, 1235587 (2013). PubMedPubMed Central Google Scholar
Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res.22, 1748–1759 (2012). CASPubMedPubMed Central Google Scholar
Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nature Rev. Genet.11, 499–511 (2010). CASPubMed Google Scholar
Qanbari, S. et al. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet.10, e1004148 (2014). PubMedPubMed Central Google Scholar
Pasaniuc, B. et al. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nature Genet.44, 631–635 (2012). CASPubMed Google Scholar
Lou, D. I. et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl Acad. Sci. USA110, 19872–19877 (2013). CASPubMedPubMed Central Google Scholar
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet.43, 491–498 (2011). CASPubMed Google Scholar
Minoche, A. E., Dohm, J. C. & Himmelbauer, H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol.12, R112 (2011). CASPubMedPubMed Central Google Scholar
Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res.18, 1851–1858 (2008). CASPubMedPubMed Central Google Scholar
Robasky, K., Lewis, N. E. & Church, G. M. The role of replicates for error mitigation in next-generation sequencing. Nature Rev. Genet.15, 56–62 (2014). CASPubMed Google Scholar
Sham, P., Bader, J. S., Craig, I., O'Donovan, M. & Owen, M. DNA pooling: a tool for large-scale association studies. Nature Rev. Genet.3, 862–871 (2002). This is a comprehensive review of pooling strategies. CASPubMed Google Scholar
Zhu, Y., Bergland, A. O., Gonzalez, J. & Petrov, D. A. Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS ONE7, e41901 (2012). CASPubMedPubMed Central Google Scholar
Kofler, R. et al. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE6, e15925 (2011). CASPubMedPubMed Central Google Scholar
Schrider, D. R., Begun, D. J. & Hahn, M. W. Detecting highly differentiated copy-number variants from pooled population sequencing. Pac. Symp. Biocomput1, 344–344 (2013). Google Scholar
Kapun, M., van Schalkwyk, H., McAllister, B., Flatt, T. & Schlötterer, C. Inference of chromosomal inversion dynamics from Pool-seq data in natural and laboratory populations of Drosophila melanogaster. Mol. Ecol.23, 1813–1827 (2014). CASPubMed Google Scholar
Kofler, R., Betancourt, A. J. & Schlötterer, C. Sequencing of pooled DNA samples (Pool-seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet.8, e1002487 (2012). This study is the first to infer TE insertion sites and the population frequency of TE insertions from Pool-seq data. CASPubMedPubMed Central Google Scholar
Sax, K. The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics8, 552–560 (1923). CASPubMedPubMed Central Google Scholar
Schneeberger, K. et al. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nature Methods6, 550–551 (2009). This paper is the first to show that Pool-seq can be used to map induced mutations. CASPubMed Google Scholar
Schneeberger, K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nature Rev. Genet.15, 662–676 (2014). CASPubMed Google Scholar
Miller, A. C., Obholzer, N. D., Shah, A. N., Megason, S. G. & Moens, C. B. RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res.23, 679–686 (2013). CASPubMedPubMed Central Google Scholar
Galvao, V. C. et al. Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J.71, 517–526 (2012). CASPubMed Google Scholar
Ehrenreich, I. M. et al. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature464, 1039–1042 (2010). This study provides proof that Pool-seq provides enough power to map complex traits. CASPubMedPubMed Central Google Scholar
Wenger, J. W., Schwartz, K. & Sherlock, G. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet.6, e1000942 (2010). PubMedPubMed Central Google Scholar
Swinnen, S. et al. Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res.22, 975–984 (2012). CASPubMedPubMed Central Google Scholar
Wade, M. J. Epistasis, complex traits, and mapping genes. Genetica 112–113, 59–69 (2001).
Earley, E. J. & Jones, C. D. Next-generation mapping of complex traits with phenotype-based selection and introgression. Genetics189, 1203–1209 (2011). CASPubMedPubMed Central Google Scholar
Bastide, H. et al. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet.9, e1003534 (2013). This papershows that Pool-seq allows highly accurate fine mapping using natural population samples. CASPubMedPubMed Central Google Scholar
Jeong, S. et al. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell132, 783–793 (2008). CASPubMed Google Scholar
Kelly, J. K., Koseva, B. & Mojica, J. P. The genomic signal of partial sweeps in Mimulus guttatus. Genome Biol. Evol.5, 1457–1469 (2013). CASPubMedPubMed Central Google Scholar
Beissinger, T. M. et al. A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics196, 829–840 (2014). CASPubMed Google Scholar
Johansson, A. M., Pettersson, M. E., Siegel, P. B. & Carlborg, O. Genome-wide effects of long-term divergent selection. PLoS Genet.6, e1001188 (2010). PubMedPubMed Central Google Scholar
Rubin, C. J. et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature464, 587–591 (2010). This is a particularly nice demonstration of the power of Pool-seq to detect selected loci in population samples. CASPubMed Google Scholar
Burke, M. K. et al. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature467, 587–590 (2010). The is the first experimental evolution study measuring allele frequency changes using Pool-seq. CASPubMed Google Scholar
Remolina, S. C., Chang, P. L., Leips, J., Nuzhdin, S. V. & Hughes, K. A. Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution66, 3390–3403 (2012). PubMedPubMed Central Google Scholar
Turner, T. L., Stewart, A. D., Fields, A. T., Rice, W. R. & Tarone, A. M. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet.7, e1001336 (2011). CASPubMedPubMed Central Google Scholar
Zhou, D. et al. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc. Natl Acad. Sci. USA108, 2349–2354 (2011). CASPubMedPubMed Central Google Scholar
Turner, T. L. & Miller, P. M. Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics191, 633–642 (2012). PubMedPubMed Central Google Scholar
Tobler, R. et al. Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol. Biol. Evol.31, 364–375 (2013). PubMedPubMed Central Google Scholar
Orozco-terWengel, P. et al. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol. Ecol.21, 4931–4941 (2012). PubMedPubMed Central Google Scholar
Reed, L. K. et al. Systems genomics of metabolic phenotypes in wild-type Drosophila melanogaster. Genetics197, 781–793 (2014). CASPubMedPubMed Central Google Scholar
Martins, N. et al. Host adaptation to viruses relies on few genes with different cross-resistance properties. Proc. Natl Acad. Sci. USA111, 5938–5943 (2014). CASPubMedPubMed Central Google Scholar
Jalvingh, K. M., Chang, P. L., Nuzhdin, S. V. & Wertheim, B. Genomic changes under rapid evolution: selection for parasitoid resistance. Proc. Biol. Sci.281, 20132303 (2014). PubMedPubMed Central Google Scholar
Magwire, M. M. et al. Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster. PLoS Genet.8, e1003057 (2012). CASPubMedPubMed Central Google Scholar
Turner, T. L., Bourne, E. C., Von Wettberg, E. J., Hu, T. T. & Nuzhdin, S. V. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genet.42, 260–263 (2010). The study is the first to show that ecologically important traits can be mapped with Pool-seq by comparing two functionally diverged populations. CASPubMed Google Scholar
Lamichhaney, S. et al. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc. Natl Acad. Sci. USA109, 19345–19350 (2012). CASPubMedPubMed Central Google Scholar
Fabian, D. K. et al. Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol. Ecol.21, 4748–4769 (2012). PubMedPubMed Central Google Scholar
Kolaczkowski, B., Kern, A. D., Holloway, A. K. & Begun, D. J. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics187, 245–260 (2011). CASPubMedPubMed Central Google Scholar
Cheng, C. et al. Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics190, 1417–1432 (2012). PubMedPubMed Central Google Scholar
Hancock, A. M. et al. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet.4, e32 (2008). PubMedPubMed Central Google Scholar
Hancock, A. M. et al. Adaptation to climate across the Arabidopsis thaliana genome. Science334, 83–86 (2011). CASPubMed Google Scholar
Fischer, M. C. et al. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Mol. Ecol.22, 5594–5607 (2013). This is a nice application of Pool-seq to find selected loci in a non-model organism. CASPubMedPubMed Central Google Scholar
Günther, T. & Coop, G. Robust identification of local adaptation from allele frequencies. Genetics195, 205–220 (2013). This paper presents the first statistical framework to identify significant associations of a given locus with one or more environmental variables using Pool-seq data. PubMedPubMed Central Google Scholar
Rubin, C. J. et al. Strong signatures of selection in the domestic pig genome. Proc. Natl Acad. Sci. USA109, 19529–19536 (2012). CASPubMedPubMed Central Google Scholar
Axelsson, E. et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature495, 360–364 (2013). CASPubMed Google Scholar
He, Z. et al. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet.7, e1002100 (2011). CASPubMedPubMed Central Google Scholar
Nolte, V., Pandey, R. V., Kofler, R. & Schlötterer, C. Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana. Genome Res.23, 99–110 (2013). CASPubMedPubMed Central Google Scholar
True, J. R., Mercer, J. M. & Laurie, C. C. Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics142, 507–523 (1996). CASPubMedPubMed Central Google Scholar
Casacuberta, E. & Gonzalez, J. The impact of transposable elements in environmental adaptation. Mol. Ecol.22, 1503–1517 (2013). CASPubMed Google Scholar
Kazazian, H. H. Jr Mobile elements: drivers of genome evolution. Science303, 1626–1632 (2004). CASPubMed Google Scholar
Boitard, S., Schlötterer, C., Nolte, V., Pandey, R. V. & Futschik, A. Detecting selective sweeps from pooled next-generation sequencing samples. Mol. Biol. Evol.29, 2177–2186 (2012). CASPubMedPubMed Central Google Scholar
Clément, J. A. et al. Private selective sweeps identified from next-generation pool-sequencing reveal convergent pathways under selection in two inbred Schistosoma mansoni strains. PLoS Negl Trop. Dis.7, e2591 (2013). PubMedPubMed Central Google Scholar
Foll, M. et al. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet.10, e1004185 (2014). PubMedPubMed Central Google Scholar
Lang, G. I. et al. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature500, 571–574 (2013). CASPubMedPubMed Central Google Scholar
Barrick, J. E. & Lenski, R. E. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol.74, 119–129 (2009). CASPubMedPubMed Central Google Scholar
Kvitek, D. J. & Sherlock, G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet.9, e1003972 (2013). PubMedPubMed Central Google Scholar
Parts, L. et al. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res.21, 1131–1138 (2011). CASPubMedPubMed Central Google Scholar
Illingworth, C. J., Parts, L., Schiffels, S., Liti, G. & Mustonen, V. Quantifying selection acting on a complex trait using allele frequency time series data. Mol. Biol. Evol.29, 1187–1197 (2012). CASPubMed Google Scholar
Bergland, A. O., Behrman, E. L., O'Brien, K. R., Schmidt, P. S. & Petrov, D. A. Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. arXiv 1303.5044 (2014).
Traverse, C. C., Mayo-Smith, L. M., Poltak, S. R. & Cooper, V. S. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proc. Natl Acad. Sci. USA110, E250–E259 (2013). CASPubMed Google Scholar
Versace, E., Nolte, V., Pandey, R. V., Tobler, R. & Schlötterer, C. Experimental evolution reveals habitat-specific fitness dynamics among Wolbachia clades in Drosophila melanogaster. Mol. Ecol.23, 802–814 (2014). PubMedPubMed Central Google Scholar
Barcellos-Hoff, M. H., Lyden, D. & Wang, T. C. The evolution of the cancer niche during multistage carcinogenesis. Nature Rev. Cancer13, 511–518 (2013). CAS Google Scholar
Merlo, L. M. F., Pepper, J. W., Reid, B. J. & Maley, C. C. Cancer as an evolutionary and ecological process. Nature Rev. Cancer6, 924–935 (2006). CAS Google Scholar
Ding, L. et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature481, 506–510 (2012). CASPubMedPubMed Central Google Scholar
Aparicio, S. & Caldas, C. The implications of clonal genome evolution for cancer medicine. New Engl. J. Med.368, 842–851 (2013). CASPubMed Google Scholar
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W. & Vogelstein, B. Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl Acad. Sci. USA108, 9530–9535 (2011). PubMedPubMed Central Google Scholar
Long, Q. et al. PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing. PLoS ONE6, e15292 (2011). CASPubMedPubMed Central Google Scholar
Kessner, D., Turner, T. L. & Novembre, J. Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol. Biol. Evol.30, 1145–1158 (2013). CASPubMedPubMed Central Google Scholar
Burke, M. K., King, E. G., Shahrestani, P., Rose, M. R. & Long, A. D. Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biol. Evol.6, 1–11 (2014). PubMed Google Scholar
Eskin, I. et al. eALPS: estimating abundance levels in pooled sequencing using available genotyping data. J. Computat. Biol.20, 861–877 (2013). CAS Google Scholar
Kofler, R. & Schlötterer, C. A guide for the design of evolve and resequencing studies. Mol. Biol. Evol.31, 474–483 (2014). CASPubMed Google Scholar
Imsland, F. et al. The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. Plos Genetics8, e1002775 (2012). CASPubMedPubMed Central Google Scholar
Del Fabbro, C., Scalabrin, S., Morgante, M. & Giorgi, F. M. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS ONE8, e85024 (2013). PubMedPubMed Central Google Scholar
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J.17, 10–12 (2011). Google Scholar
Nevado, B., Ramos-Onsins, S. E. & Perez-Enciso, M. Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics. Mol. Ecol.23, 1764–1779 (2014). CASPubMed Google Scholar
Degner, J. F. et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics25, 3207–3212 (2009). CASPubMedPubMed Central Google Scholar
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res.20, 1297–1303 (2010). CASPubMedPubMed Central Google Scholar
Koboldt, D. C. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics25, 2283–2285 (2009). CASPubMedPubMed Central Google Scholar
Bansal, V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics26, i318–i324 (2010). CASPubMedPubMed Central Google Scholar
Zhou, B. Y. An empirical Bayes mixture model for SNP detection in pooled sequencing data. Bioinformatics28, 2569–2575 (2012). CASPubMed Google Scholar
Chen, Q. & Sun, F. A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. BMC Genomics14 (Suppl. 1), S1 (2013). PubMedPubMed Central Google Scholar
Druley, T. E. et al. Quantification of rare allelic variants from pooled genomic DNA. Nature Methods6, 263–265 (2009). CASPubMedPubMed Central Google Scholar
Vallania, F. L. et al. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res.20, 1711–1718 (2010). CASPubMedPubMed Central Google Scholar
Wei, Z., Wang, W., Hu, P., Lyon, G. J. & Hakonarson, H. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res.39, e132 (2011). CASPubMedPubMed Central Google Scholar
Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv 1207.3907 (2012).
Calvo, S. E. et al. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nature Genet.42, 851–858 (2010). CASPubMed Google Scholar
Fiston-Lavier, A.-S., Barron, M. G., Petrov, D. A. & González, J. T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. bioRxivhttp://dx.doi.org/10.1101/002964 (2014).
Zhuang, J., Wang, J., Theurkauf, W. & Weng, Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res.42, 6826–6838 (2014). CASPubMedPubMed Central Google Scholar
Kofler, R., Pandey, R. V. & Schlötterer, C. PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-seq). Bioinformatics27, 3435–3436 (2011). CASPubMedPubMed Central Google Scholar
Boitard, S. et al. Pool-HMM: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples. Mol. Ecol. Resour.13, 337–340 (2013). PubMedPubMed Central Google Scholar
Ferretti, L., Ramos-Onsins, S. E. & Perez-Enciso, M. Population genomics from pool sequencing. Mol. Ecol.22, 5561–5576 (2013). PubMed Google Scholar
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population genomics. Mol. Ecol.22, 3124–3140 (2013). PubMedPubMed Central Google Scholar
Vitalis, R., Gautier, M., Dawson, K. J. & Beaumont, M. A. Detecting and measuring selection from gene frequency data. Genetics196, 799–817 (2014). PubMed Google Scholar
Gautier, M. & Vitalis, R. Inferring population histories using genome-wide allele frequency data. Mol. Biol. Evol.30, 654–668 (2013). CASPubMed Google Scholar
Feder, A. F., Petrov, D. A. & Bergland, A. O. LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data. PLoS ONE7, e48588 (2012). CASPubMedPubMed Central Google Scholar
Minevich, G., Park, D. S., Blankenberg, D., Poole, R. J. & Hobert, O. CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. Genetics192, 1249–1269 (2012). CASPubMedPubMed Central Google Scholar
Edwards, M. D. & Gifford, D. K. High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics13 (Suppl. 6), S8 (2012). PubMedPubMed Central Google Scholar
Bowen, M. E., Henke, K., Siegfried, K. R., Warman, M. L. & Harris, M. P. Efficient mapping and cloning of mutations in zebrafish by low-coverage whole-genome sequencing. Genetics190, 1017–1024 (2012). CASPubMedPubMed Central Google Scholar
Austin, R. S. et al. Next-generation mapping of Arabidopsis genes. Plant J.67, 715–725 (2011). CASPubMed Google Scholar
Leshchiner, I. et al. Mutation mapping and identification by whole-genome sequencing. Genome Res.22, 1541–1548 (2012). CASPubMedPubMed Central Google Scholar
Prosperi, M. C. & Salemi, M. QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinformatics28, 132–133 (2012). CASPubMed Google Scholar
Zagordi, O., Bhattacharya, A., Eriksson, N. & Beerenwinkel, N. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics12, 119 (2011). PubMedPubMed Central Google Scholar
Eyre, D. W. et al. Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. PLoS Comput. Biol.9, e1003059 (2013). CASPubMedPubMed Central Google Scholar
Astrovskaya, I. et al. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics12 (Suppl. 6), S1 (2011). PubMedPubMed Central Google Scholar
Yang, X., Charlebois, P., Macalalad, A., Henn, M. R. & Zody, M. C. V-Phaser 2: variant inference for viral populations. BMC Genomics14, 674 (2013). CASPubMedPubMed Central Google Scholar
Töpfer, A. et al. Viral quasispecies assembly via maximal clique enumeration. PLoS Comput. Biol.10, e1003515 (2014). PubMedPubMed Central Google Scholar
Töpfer, A. et al. Probabilistic inference of viral quasispecies subject to recombination. J. Comput. Biol.20, 113–123 (2013). PubMedPubMed Central Google Scholar
Prabhakaran, S., Rey, M., Zagordi, O., Beerenwinkel, N. & Roth, V. HIV haplotype inference using a constraint-based Dirichlet process mixture model. Machine Learning in Computational Biology NIPS Workshop (2010). Google Scholar
Pandey, R. V., Kofler, R., Orozco-terWengel, P., Nolte, V. & Schlötterer, C. PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila. BMC Genet.12, 27 (2011). CASPubMedPubMed Central Google Scholar
Chen, X., Listman, J. B., Slack, F. J., Gelernter, J. & Zhao, H. Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples. Genet. Epidemiol.36, 549–560 (2012). PubMedPubMed Central Google Scholar
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nature Methods11, 396–398 (2014). CASPubMedPubMed Central Google Scholar