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Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale.
This has been integrated with sequence reads generated by a scalable, highly parallel sequencing by synthesis (SBS) method with throughput significantly greater than capillary electrophoresis.
Since highly parallel sequencing was used for this approach, which produced many, but short reads (100 bp), we have set up an appropriate bioinformatic analysis pipeline that allows to reliably extract in-depth functional and taxonomic information from this dataset.
Margulies et al. [ 40] recently described a highly parallel sequencing by synthesis approach that demonstrated an increased throughput for sequencing of genomic DNA.
SNP discovery by highly parallel sequencing was successfully demonstrated in cattle [ 15], in which reduced-representation pooled libraries were sequenced using the Illumina/Solexa technology.
We have generated more than 300,000 novel C. elegans EST sequences by this highly parallel sequencing method for this study.
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Especially, with the increase of the output of highly parallel sequences and the decrease of the cost per run, it is more feasible to get deep sequences for multiple individual genotypes or pooled samples.
In MPSS the tags are amplified, loaded onto a microbead library, and immobilized in a flow cell for automated highly-parallel sequencing [ 3].
So-called next-generation sequencing technologies (Roche/454, Illumina/Solexa, AB/SOLiD, Helicos/Heliscope) leverage highly parallel shotgun sequencing to deliver multiple short sequences from input DNA.
Highly parallel RNA sequencing methods have recently helped to gain insights into the global modulation of mRNA 3′end processing.
Indeed, next-generation 454 sequencing allows highly parallel DNA sequencing that is many orders of magnitude faster than standard sequencing methods and increase sequencing depth and coverage while reducing time, labour and cost [7].
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