Next Generation Sequencing: Era of short reads

I thought that I should do a brief introduction on Next Generation Sequencing (NGS) before my next post.

Next Generation Sequencing is, as the name infers, a new DNA sequencing technology compared to the traditional sequencing (Sanger sequencing).When people ask me what’s the difference between NGS and Sanger, I’ll say no cloning, cheaper, higher accuracy, higher throughput in one breath! However, NGS produce shorter reads compared to Sanger sequencing.

The NGS platforms that are currently running in the labs are 454 GS-FLX Titanium (replacing GS-FLX), Illumina Solexa GAII (Will be replaced by GAIIx) and ABI SOLiD 3. 454 sequencing is the only NGS technology that can sequence up to 400bp but it has lower throughput compared to the rest (180Mb/run for GS-FLX Titanium). Both Solexa and SOLiD is expected to achieve 100bp in length and up to 10 Gb/run this year. Among the applications of NGS are whole genome sequencing, transcriptome sequencing, gene expression (RNA-seq), microRNA, Chip-Seq etc.

Despite all the advantages of NGS technology, the main challenge when handling short reads is bioinformatics. The assembly of short reads will produce more contigs due to repeats problem. Again don't want to elaborate on that.

I would recommend this paper by Elaine Mardis. It’s a very comprehensive review on NGS. Please bear in mind that most paper in 2006 will compare Sanger and 454 sequencing. After the emergence of Illumina Solexa and ABI SOLiD in 2007, the papers would compare all 3 platforms. For those who are interested to know more about the challenges of NGS, click here to check out October 2008 issue of Nature Biotechnology.