A possible solution is a hybrid assembly constructed with a mixture of shallow coverage (~5×) of mate-pair long-reads with deeper coverage (~25×) of paired-end short-reads (Schatz et al. 2010; Gnerre et al. 2011).
BAC end sequences are one of several possible sources of shallow coverage, genome-wide, long DNA reads.
Semirandom sampling of sorghum sequences led to shallow coverage, by uniquely aligning reads, of one third of the genome, the same proportion as is classed [ 4] as nonrepetitive.
Based on our distribution of number of sequences obtained from each species, we would expect the specimen with the most shallow coverage among the 50 specimens to have a coverage of 11×.
Students are also stymied by "repeated, shallow coverage" that fails to give them a conceptual understanding of what it means to do science.
This problem is exacerbated when shallow coverage is obtained for normal samples, leading to a greater number of false somatic SV predictions in the tumor sample.
The 'many genes one individual' approach is of course an extreme, and in reality, pooled population resequencing with shallow coverage may become the most widely adopted approach (see e.g. Jones et al. 2012; Lamichhaney et al. 2012).
Many more wildlife genome projects are underway and intend to provide only shallow coverage.
Only sites with QUAL > 50 for deep-coverage or QUAL > 20 for shallow coverage were considered as potentially variable sites.
