Assisted by Poul Liboriussen, System Developer at CLC bio, a team of researchers headed by Christopher M. Seabury used our de novo assembly algorithm for a project providing the draft genome for the Scarlet Macaw parrot.
The studies of this avian genome showed that high quality de novo genome assemblies can be generated at low costs. A whole genome analysis of divergence suggested putative candidate genes for parrot traits of interest such as intelligence, speech and longevity, with independent human GWAS studies lending support to these findings.
Poul engineered improvements to the original de novo assembly algorithm, especially related to scaffolding. Later on, he helped the researchers understand the mechanics of the de novo assembly process by providing details about the algorithm.
CLC Genomics Workbench was used by Seabury and his team for both quality trimming of sequencing reads and performing the de novo hybrid assembly using scaffolding.
Seabury and his team also found alternative usage of our large gap read mapper algorithm. They used it for estimating concordance between assemblies and to consider scaffolded versus unscaffolded assemblies. Please note that this approach naively applied may not work optimally for certain assemblies, especially regarding repetitive regions.Read the interesting paper
A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)
Seabury CM, Dowd SE, Seabury PM, Raudsepp T, Brightsmith DJ, et al.
PLoS ONE 8(5): e62415. doi:10.1371/journal.pone.0062415 (2013)