Usually, NGS is done on pools of samples. Hence a lane can contain a mixture of libraries which need to be extracted into their corresponding samples. We use illumina's bcl2fastq software for most converting the bcl files to fastq files.
Sequencing Quality Assessing
At the McDermott Center, we are most careful about the quality of data generated by the sequencers. The first check is to make sure we have enough sequencing reads for the analysis. Other parameters include % Passing Filter, Mean Quality Score and % of >=Q30 Bases to name a few.
For an overiew on how illumina sequenicng technology works, please visit the link.