De Novo Sequencing by Next-Generation Sequencing

De novo sequencing is typically accomplished by assembling individual sequence reads into longer contiguous sequences (contigs) or correctly ordered contigs (scaffolds) in the absence of a reference sequence.

Methods for De Novo Sequencing
Historically, de novo sequencing was carried out using capillary electrophoresis (CE) sequencers. With its long read lengths and high accuracy, CE-based sequencing made overlap consensus assembly the gold-standard technology for de novo projects. However, more recently, the high-throughput capabilities of massively parallel sequencing and the development of short-read assemblers have significantly reduced the time and cost associated with sequencing an entire genome.

he accuracy and throughput of the 5500xl Genetic Analyzer enables unparalleled de novo assembly of novel genomes, opening the way to detailed genetic analysis of any organism.

• Accuracy—ultra-deep sequencing capability combined with industry-leading, highly accurate 2-base color coding, plus Exact Call Chemistry (ECC), enables short-read assembly with less coverage
• Flexible file output—output files in base space or color space enable you to use the short-read assembler of your choice
• Throughput—generate over 20 Gb of sequence per day and get the coverage you need for high-confidence assembly
• Flexible library format—long-insert 2 x 60 mate pairs with your choice of insert size from 1 kb–6 kb, paired end reads, fragment reads, or a combination of library approaches, the flexible format FlowCells allow you to run them all simultaneously
• Coverage—long-insert mate pairs, ultra–high-throughput and industry-leading accuracy give you superior coverage to get more genomes sequenced, faster