Preliminary genome assemblies were generated by two assemblers designed for de novo assembly of next-generation sequencing data [ 59], the CLC Workbench assembler (CLC bio, Denmark) and the Newbler assembler (version 2.3), with different input data content and assembling strategies (in Additional file 1: Table S1).
Statistics of the assemblies were generated by perl scripts using BioPerl modules.
Illumina-PacBio hybrid assemblies were generated by AHA [ 55] and CABOG (using pacBioToCA error correction by Illumina reads) [ 56].
As for the Illumina sequencing described earlier, combined assemblies were generated by relinearization of the reference and the consensus base call at each site was used.
We note here that, in addition to our previous predictions, our new coordinated assembly model has allowed the additional prediction that phase precession would be severely disrupted following remapping if CA1 assemblies were generated by coordinated coding.
> -wrap-foot> aAdditiveffectct of the P. integrifolia allele bPercentage of variation explained High quality transcriptome assemblies were generated by RNA-seq data from three Petunia spp. and these were mined for molecular markers and plastochron-related transcripts.
Reference assemblies were generated by aligning filtered reads against the D. melanogaster genome following methods described by Lack et al. [ 62], an assembly pipeline that adds an intermediate realignment step for the purpose of aligning reads around insertion and deletion sites.
Discrete self-assemblies are generated by the combination of a variety of palladium II) components and ligands ranging from bi- to polydentate.
The initial transcriptome assembly was generated by assembling the Illumina reads using the CLC Workbench assembler.
Final genome assembly was generated by the Newbler assembler on all Roche/454 reads, selected Illumina reads (paired and unpaired reads for the 200 bp library, paired reads for the 500 bp library), and SOLiD reads (in Additional file 1: Table S1).
DNA for nucleosome assembly was generated by PCR using plasmid pGEM3Z-601 as a template, which codes for a high-affinity nucleosome positioning sequence [30].
