Since the depletion did not work out for L. y-signata, a much deeper sequencing was performed in the second sequencing run as described above.
Likewise, inclusion of the highly variable densities of SNPs discovered from Cinnamon's much deeper sequencing would reflect this cat's particular pattern of homozygous and heterozygous regions.
First, assembling and scoring heterozygous reads is difficult and requires much deeper sequencing than required if simply scoring homozygous SNPs (Langley et al. 2011).
Much deeper sequencing will be needed to ensure complete or sufficient coverage of the selected fragments, in comparison to unbiased selection techniques such as PCR.
454 FLX Titanium is a massive pyrosequencing strategy which generates medium-size single reads uncovering large amounts of DNA sequences providing much deeper sequencing coverage than it is possible with conventional Sanger sequencing [ 40].
A more efficient implementation of the base quality recalibration and error inference algorithms vastly reduces run time and memory use, making it possible to analyze much deeper sequencing data.
As we note below, realizing that the data set could serve as a gold standard (and indeed is being used by several labs already), we decided to leverage the advances in sequencing yields, to generate much deeper sequencing and better analysis.
VI) Sequencing is done using Illumina technology, allowing for a much deeper sequencing and the possibility to obtain paired-end information The whole transcriptome RNAseq protocol was developed to determine operon structures, so far unknown transcripts as well as transcript ends.
In fact, despite having a much deeper sequencing coverage, the draft genome assembly using male reads alone has a smaller N50 length (the scaffold size above which 50% of the total length of the sequence assembly can be found, Table 1) than that derived from female reads (9.9 kb vs. 12.6 kb).
