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Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth.
Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species.
Next-generation (massively parallel, or second-generation) sequencing technologies have largely supplanted first-generation technologies.
However, only a limited number of species have been completely sequenced due to the inherent limitations of second-generation sequencing technologies, including GC-bias and the inability to resolve large structural variations.
Furthermore, the increased use of second-generation sequencing technologies with short read lengths means that much of future metagenomic data will be error-prone.
The increased read length of the second-generation sequencing technologies could potentially overcome most of the disadvantages mentioned above.
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Ganal et al. [ 12] reviewed recent SNP identification methods including DNA arrays, amplicon sequencing, mining existing EST resources, and using sequence data generated with second generation sequencing technologies.
Additionally, haplotype determination has been aided by DNA strand specific or genomic phase-based information generated using second generation sequencing technologies since each sequencing read is from only one homologous chromosome and not a consensus of the two [ 24].
Given massively parallel second generation sequencing technologies [ 1- 3], huge collection of data are being generated for a wide diversity of regulatory elements genome-wide (such as transcription factors, epigenetic marks, genetic variants, DNaseI hypersensitivity, and transcriptomes).
With the advent of the second generation sequencing technologies [ 1], more and more sequences are being generated on a daily basis from various organisms in order to analyze genome sequences, whole transcriptomes, molecular evolution, and metagenomes (reviewed in [ 2- 7]).
Recent advances in second generation sequencing technologies have allowed us to take this one step further: sequence-based identification of pathogens and of their virulence characteristics.
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