Using the gender difference to compute the relative k-mer coverage of the sex chromosome, we estimated the cff-DNA concentrations, which denote as ε.
A genome-independent transcriptome was assembled using Trinity (trinityrnaseq_r2012-06-08) [ 97] with minimum k-mer coverage of 2 and default parameters.
Consideration of the K-mer coverage of contigs in both assemblies revealed a restricted number of relatively short contigs with atypical coverage.
Scalpel applied the standard formula for the Chi-Square statistics and applied to the K-mer coverage of both alleles of an INDEL.
A de novo transcriptome assembly was carried out with the latest version of the Trinity program (trinityrnaseq_r20140413), with a minimum k-mer coverage of 2 [ 14].
Trinity was run using default settings, with a minimum k-mer coverage of 1, resulting in an assembly with 420,978 contigs.
When no coverage cutoff is specified, ABySS determines the coverage cutoff automatically according to the actual k-mer coverage of each respective sequence.
Assemblies were made using Velvet 0.7 [ 21] with a range of hash lengths from 33 to 63 and a minimum k-mer coverage of 5×.
For L. newyorkensis, contigs representing small and large subunit ribosomal DNA sequences had K-mer coverage of 328 and 385, respectively, with the median K-mer coverage of all contigs being 55, consistent with the presence of 6 or 7 copies of the ribosomal repeat.
It is informative to consider the n-mer coverage of a random pseudo-human genome of the same length as the human genome and with the nucleotides A, C, G, and T appearing with equal frequency in the genome.
For the use in Overlap Layout Consensus (OLC) assemblers, the data set was digitally normalized to a k-mer coverage of 20 using tools from the khmer package (Pell et al. 2012).
