Alex Van Dam
,
Department of Systems Biology, Eukaryotic Molecular Cell Biology, Denmark Technical University, Kgs. Lyngby, Denmark
Simon Rasmussen
,
Department of Systems Biology, Center for Biological Sequence Analysis, Denmark Technical University, Kgs. Lyngby, Denmark
Bent Petersen
,
Department of Systems Biology, Center for Biological Sequence Analysis, Denmark Technical University, Kgs. Lyngby, Denmark
Rubini Kannangara
,
Chr. Hansen A/S, Hørsholm, Denmark
Paiman Khorsand-Jamal
,
Chr. Hansen A/S, Hørsholm, Denmark
Bjoern Madsen
,
Chr. Hansen A/S, Hørsholm, Denmark
Finn Okkels
,
Chr. Hansen A/S, Hørsholm, Denmark
Mads Bennedsen
,
Chr. Hansen A/S, Hørsholm, Denmark
Kim Binderup
,
Chr. Hansen A/S, Hørsholm, Denmark
Thomas Sicheritz Pontén
,
Department of Systems Biology, Center for Biological Sequence Analysis, Denmark Technical University, Kgs. Lyngby, Denmark
Ulf Thrane
,
Department of Systems Biology, Fungal Physiology and Biotechnology, Denmark Technical University, Kgs. Lyngby, Denmark
Birger Lindberg Møller
,
Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
Uffe Mortensen
,
Department of Systems Biology / Eukaryotic Molecular Cell Biology, Denmark Technical University, Kgs. Lyngby, Denmark
Rasmus Frandsen
,
Department of Systems Biology / Eukaryotic Molecular Cell Biology, Denmark Technical University, Kgs. Lyngby, Denmark
The cochineal insect genome assembly is described. ALLPATHS-LG was used for the initial assembly of Illumina short-read genomic data. Then RNA-seq data was used to merge scaffolds from the ALLPATHS-LG assembly. Trinity was used to reconstruct a de-novo transcriptome used by L_RNA_scaffolder to merge and orient scaffolds from the ALLPATHS-LG assembly. Next BWA was used to align all of the RNA-seq data to the new L_RNA_scaffolder assembly. The BWA alignment was then used to further merge scaffolds using Opera. We then used REAPR to find errors in the Opera genome assembly. Finally a PacBio data set is planned for a hybrid assembly to close the genome.
