![]() However, PCR methods can introduce artifacts 14, 15, yield non-specific products 16, and are limited to enriching for sequences up to ~10 kb. A common enrichment strategy is PCR, in which primers specifically amplify a target sequence from a heterogeneous mixture. ![]() This can greatly improve assemblies and has been used to address questions ranging from deconvoluting cancer heterogeneity 12 to finding gene clusters encoding new, useful molecules in the microbiome 13. Often, useful contigs can only be generated for the most abundant organisms, and the overwhelming majority of species present at low and moderate levels are missed 10.Īn effective means to overcome the challenges introduced by short read data is to enrich for target sequences prior to sequencing 11. Here, however, the shortness of the reads, sparseness of the sampling, and massive diversity of the system impose technical challenges, making assembly difficult and error-prone 4, 9. To extract meaningful biological insight from the short read data requires “assembling” reads into “contigs” spanning the relevant genetic length scale. Genetic structures like genes, gene clusters, and genomes typically span much longer scales, from kilobases to gigabases of sequence 5, 6, 7, 8. Moreover, even the highest throughput modern sequencers are capable of sampling just a minute fraction of the sequences present in most systems, and the “reads” are obtained in the form of short, ~100 base fragments 2, 3, 4. A single ocean sample, for example, can contain billions of microbes, each with its own genes, gene clusters, and genomic structure 1. However, the massive heterogeneity present in most systems also imposes technical challenges to their characterization. ![]() Heterogeneity is an important aspect of many biological systems, impacting their ability to respond to stimuli or evolve against evolutionary stresses. ![]()
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