Paired read support is available but before it can be used, the read files need to be combined using the pairing operation. For example, if you have imported two FASTQ files, one with forward reads and one with reverse reads, you should select both and then use Sequence→Set Paired Reads... and choose the appropriate settings such as expected distance between pairs. This will generate a new paired file which can be selected in the assembly operation and the extra information will be used to help the assembler resolve complex placement issues.
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