I have 11 mpileups generated by novoalign from whole genome sequencing of Daphnia, which has a genome size of ~200MB. Each is the result of alignment of about 130M paired-end illumina reads. I find that all of the mpileups have about 110M lines, implying that we have info for about 55% of the reference. I want to quantify the degree of overlap in coverage among the mpileups. Is there an easy way to do this with samtools or something similar? Also, is there a way to construct an mpileup file that has a line for every site in the reference, rather than just those with read coverage?
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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