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Each string produced by a sequencing machine is referred to as a "read," and thousands of overlapping reads are created for every genome.
Additionally, in a preliminary alignment to genome, overlapping reads were aggregated together into contiguous intervals.
Illumina paired-end sequencing of the amplified sequences generates millions of overlapping reads.
Computational methods have been developed to reconstruct transcript structures based on overlapping reads [36].
The extraction of overlapping reads with proper primer sequences and correct sequence tags was performed with a custom Perl program.
Our approach builds on preparing libraries with tunable size distributions such that sequencing from both ends generates overlapping reads.
The ability to assemble overlapping reads into reliable contigs is also crucial for de novo genome sequencing applications.
Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads.
Using the clone contigs, we restrict the search for overlapping reads to a small set of neighboring clones.
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As such, completely-overlapping reads can be achieved when performing paired-end sequencing.
We also assembled the merged reads together with the non-overlapping reads (Group A [PE + SE]).
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