Most DNA applications do not have a standard choice of sequencing length and depth as these parameters vary widely depending on the goals of the project, the organism being sequenced, and the application itself. The few applications with standard sequencing conditions are shown below. For all sequencing options, please visit our sequencing technologies page.
|Sequencing Application||Standard Sequencing Condition||Standard Reads or Coverage|
|ChIP-Seq||50bp SE||25M SE|
|WGS||150bp PE||30X on HiSeq X|
|Exome||100bp PE||Varies; 65X, 85x, or 100x|
|Mate pair||100bp PE or 150bp PE||Varies; 30X on HiSeq X|
All demultiplexing (i.e. the sorting of indexed reads) is included in the cost of basic sequencing, with users receiving fastq files for each sample. Additional fees are charged for some types of analysis, including alignment.
For a fee, WGS data may be aligned to a reference genome if one is available. Human WGS data may be aligned and variant called using the DRAGEN platform, and WGS and vcf metrics calculated.
Exome sequencing data is aligned to the 1000 Genomes reference GRCh37 or hg19 by the DRAGEN platform and capture metrics are calculated. Bam/bai/vcf files or fastq files may be provided as results. For an extra fee, samples can be variant called using the Broad’s GATK pipeline which will add several weeks to the analysis time.
The HudsonAlpha Discovery uses Illumina's Nextera Mate Pair kit for construction of mate pair libraries. It offers a gel-free (non-size selected) protocol to use when input DNA is limiting and a size-selected protocol to generate mate pair libraries of size ranges 3-5kb, 5-7kb, or 7-10kb. Mate pair libraries may be sequenced on all Illumina sequencers. The fastq files require special processing before use in alignment or assembly analysis. This technical note from Illumina describes the mate pair library construction and data processing required. Adapter sequences used in mate pair library preparation may be found here.
HudsonAlpha Discovery provides options for both basic analysis as well as advanced data analysis for many DNA sequencing applications. All analysis begins with one-on- one discussion between our analysis team and customers to better understand their experimental set-up, objectives and requirements. The basic analysis is available as fee-for-service, with customers paying for staff time as well as computational time. Fee-for-service analysis includes alignment to either a standard genome or installation and alignment to a non-standard genome. Any further advanced analysis, such as assembly, peak calling, or variant calling, becomes collaborative, with customers acknowledging staff members’ contributions and expertise with appropriate authorship on manuscripts. Fees for basic analysis will still be applied for all collaborative projects.