Implement contig coverage

[cjfields]

This is actually a multistage process. We want to add some basic read coverage information for the assembled contigs by aligning reads back to them to assess read depth. This will require alignment of reads to the contigs (recommend using bwa here), followed by coverage estimation. This can be tested via command line using example tools and data.

[cjfields]

Task can use unaligned reads and align back to assembly genome, generate coverage stats