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Many assemblers have been developed to assemble reads generated by Next Generation Sequencing platforms (NGS).
The millions of short sequence reads generated by Next Generation Sequencing (NGS), like the SOLiD (AppliedBiosystems) and Illumina Genome Analyzer, are particularly useful for small RNA transcription profiling.
Ψ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology.
In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form.
First the 3′ end adapters of reads generated by Illumina Genome Analyzer IIx were trimmed using The Flexible Barcode and Adapter Remover (FLEXBAR, Dodt et al., 2012).
In addition, sequence reads generated by the Syngenta rice genome sequencing project (Goff et al. 2002) were assembled and used to extend contigs.
To aid in the analysis of both short tandem repeat (STR) and single nucleotide polymorphisms (SNP), we have designed a new program called SEQ Mapper to search for genetic polymorphisms within a large number of reads generated by MPS.
Sequencing was bidirectional with approximately 57% of reads generated by the forward (5') primers and 43% of reads generated by the reverse (3') primers.
Table 1 provides a combined summary analysis of sequence reads generated by Sanger and 454 pyrosequencing.
A genome-wide quantification of mapped reads generated by standard SCS or bareback-processing corroborates these findings (Fig. 4c).
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.
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