De novo Genomic Assembly


NGen is equally adept at de novo assembly of Roche 454 and paired-end Illumina sequence data. The quality of the de novo assembly is assessed by size and accuracy of contigs that are created.


De novo Genomic Assembly
De novo Genomic Assembly

 

 

NGen Assembly Report
NGen Assembly Report

 

 

Strategy View (click to enlarge image)
Strategy View (Fig C)

 

 


De novo assembly of Roche 454 Life Sciences data yields large and accurate contigs, as seen in the first image.  In a typical microbial genome assembly, Contig N50 (the size contig at which 50% of the sequence data is represented) values exceed 80K base pairs and genome coverage is attained in less than 100 contigs. In many assemblies, contig N50 exceeds 100K with genome coverage attained in 25 contigs. If paired-end end Roche 454 Life Sciences data is used, contigs can be ordered into a handful of large scaffolds to attain genome coverage that greatly facilitates gap closure and completion of the genome assembly.


The Lasergene application provides a strategy view that allows researchers to view contig scaffolds along with the paired sequence reads that tie contigs together, which is shown in the bottom image. Sequence pair data is represented by a user-defined color scheme as well as a pair consistency histogram plot to identify regions that are consistent or inconsistent with the paired-end information.


Additional information on Reference Guided Assembly

Additional information on "Deep" Assembly

Additional information on RNA-Seq, SAGE and DGE Data Assembly