On read sequencing libraries, the opposite strands are considered on the files? (and how are they handled on assembly?)

Question

[v.berriosfarias]

Just want to know if on my paired end reads fastq files are considered the opposite strand, Does on the sequencing procedure the opposite DNA strands discarded or are they sequenced too? if the are sequenced, how are the opposite DNA strands handled on contig assembly steps?

[GenoMax]

Nucleic acid fragments are made into sequence ready libraries. Each of these library fragments is being sequenced from both ends in paired-end sequencing. As you recall, sequencing always occurs in 5' --> 3' direction on respective strands.