Equally delicious is the author's running commentary on her own words — Fisher edited the book extensively in 1951, and the 1988 edition that I am reading incorporates these changes into the text as afterthoughts in brackets.
SHAPEIT2 [ 51] adds the ability to incorporate molecular information from sequence reads, incorporating calls and base-quality scores in a probabilistic model.
As expected for the perfect assemblies, as read coverage increased, the percentage of reads incorporated into the assembly grew to near 100%.
See Additional file 1: Table S1 for the size of the RNA-Seq datasets and the number of reads incorporated into a de novo transcriptome assembly.
Figure 1(a) shows contig and c-isotig counts as well as percent of reads incorporated into the assemblies as sequencing depth increases.
Perl and Matlab scripts were also used to, collate the results of different BLAST searches for each sequence read, incorporate marker information, and assemble the genome zipper.
As Trinity does not report the specific reads incorporated into assembled transcripts, we aligned all reads back to the final Trinity assemblies with alignRead.pl script of the Trinity package using Bowtie [ 35] allowing us to scale protein annotation by contig coverage.
