Demultiplexing and FASTQ Generation

Sequencing data stored in BCL format are processed through the bcl2fastq conversion software. The bcl2fastq conversion software demultiplexes data and converts BCL files to standard FASTQ file formats for downstream analysis. For each sequencing run, the VeriSeq NIPT Assay Software creates a sample sheet (SampleSheet.csv). This file contains sample information provided to the software during the sample prep process (using the software API). These sample sheets contain a header with information about the run and descriptors for the samples processed in a particular flow cell.

The following table provides sample sheet data details.

Column Name	Description
SampleID	Sample identification.
SampleName	Sample name. Default: same as SampleID.
Sample_Plate	Plate identification for a given sample. Default: blank.
Sample_Well	Well identification on the plate for a given sample.
I7_Index_ID	Identification of the first index adapter.
index	Nucleotide sequence of the first adapter.
I5_Index_ID	Identification of the second adapter.
index2	Nucleotide sequence of the second adapter.
Sample_Project	Project identification for a given sample. Default: blank.
SexChromosomes	Analysis pertaining to sex chromosomes. One of the following: • Yes–Sex chromosome aneuploidy and sex reporting requested. • No–Neither sex chromosome aneuploidy nor sex reporting requested. • SCA–Sex chromosome aneuploidy reporting requested, sex reporting not requested.
SampleType	Sample type. One of the following: • Singleton–Single embryo pregnancy. • Twin–Multiple embryo pregnancy. • Control–Control sample of known sex and aneuploidy classification. • NTC–No template control sample (no DNA).