Illumina Sequencing
This section provides information and answers questions related to Illumina sequencing and SEQuoia Express.
This SEQuoia Express Toolkit is designed to analyze the the data produced by the library prep kit.
For a more details about how the toolkit works and what it does see the user guide: SEQuoia Express analysis toolkit.
The diagram below shows the structure of the fragment that is generated by the library preparation kit. Sequencing primers bind at the R1 and R2 sites and sequencing proceeds inward toward the fragment.
If you are using PhiX spike in for sequencing refer back to the Illumina documents here. PhiX sequences are removed from samples during demultiplexing.
If you chose to multiplex your reads, the demultiplexing should be done by the bcl2fastq software for your reads using your sample sheet provided for the Illumina sequencing run. If the samples were run across multiple sequencing lanes and lane-split FASTQ files are generated for each sample, you can run the SEQuoia Express Toolkit on each sample+lane separately to get lane-specific QC metrics for the sample. If lane-split FASTQ files are provided, most likely you will want to use bash or some other means to concatenate your files so all the reads for a specific sample are merged in to one set of FASTQ files for each sample.
Caution the SEQuoia Express Toolkit processes all FASTQ files in a directory provided to it. Thus, if you merge FASTQ files, moving the unmerged versions to a different directory will prevent duplicate analyses.