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Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
(Magoč and Salzberg, 2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics.