Whole and Targeted Genome Sequencing Analysis    

Whole genome sequencing generates the most comprehensive sequence dataset for an individual organism and allows detailed evaluation of all genetic variations on in an individual or strain. While it is a preferred and cost-effective approach for smaller prokaryotic and eukaryotic genomes, the sheer scale of the vertebrate and plant genomes necessitates a substantial investment in bioinformatics / data mining in order to achieve an effective translation of this information into genetic medicine and clinical diagnostics. For this reason, many researchers prefer targeted genome re-sequencing, where a selected subset of genomic sequence (for example, an “exome”) is extracted and analyzed.

De novo assembly of prokaryotic genomes

De novo sequencing, in which sequencing analysis is performed without the aid of a reference genome, is necessary when sequencing a novel species or novel DNA sequence, e.g. a cancer sample. In this application, overlapping sequences are assembled into contigs. Because Illumina TruSeq technology tends to optimize for a large number of shorter reads, de novo sequencing with this platform requires 100-fold or more genome coverage (see Important Considerations) in order to insure a minimal number of gaps. Thus, the GAIIx is best suited for generating de novo genome sequences for organisms with smaller genome sizes, primarily for bacteria and viruses (see Table 1).

Genome Re-sequencing

If a reference sequence of the genome is available, your sample can be sequenced at a lower coverage level (see Table 1) and the reads mapped to the reference. This is an excellent approach for identifying SNPs and indels in your samples!

Targeted Sequencing

At ACGT, Inc. we offer our services in preparing targeted exome libraries using Agilent Technologies SureSelect products. We can also sequence customer prepared targeted sample libraries constructed using any number of methods including other commercial kits.

Table 1. Genome Size vs Fold Coverage

* 7 lanes is maximum per 1 flow cell