Sequence alignments against the P. taeda v1.01 draft genome assembly were generated to compare transcript to genome mapping of the P. patula v1.0 transcriptome assembly to that of other Pinus transcriptomes.
The transcriptome assembly was generated to reveal the first picture of its gene content.
A preliminary view of the ICPA 2039 assembly was generated to check the connections between the scaffolds and for the removal of contaminants (Fig. 1).
To confirm that the apparent absence of an IR was not a genome assembly artifact, PCR amplicons were generated to verify the region around the single rRNA operon.
Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches.
Multiple assemblies were generated with varying parameters to account for potential gene collapse or artificial duplication/expansion, which is a significant problem for regions with shared sequence or many repeats.
Assemblies were generated using the de novo assembler Velvet v1.2.10 [ 24], with optimal kmer choice for each read set refined through iterative calls to VelvetOptimiser v2.2.5 [ 48].
To better visualize assembly-correctness, dot plots for these five assemblies were generated.
De novo assemblies were generated for each read set using Velvet (version 1.2.03) and VelvetOptimiser, with each read set mapped back to each assembly (Zerbino & Birney, 2008).
All assemblies were generated using Phrap.
