Check physical coverage
The physical coverage can be evaluated when analyzing paired-end or mate paired libraries, in order to measure the coverage between pairs.
Drops in physical coverage can be used to spot mis-assembled contigs.
In the repository a simulated mate paired library has been aligned and the sorted BAM file is available in test/mp.bam.
Command:
covtobed --physical-coverage --min 10 test/mp.bam
The output (below) is formatted as a regular BED file, but contains the physical rather than the sequence coverage in the fourth column:
NC_001416.1 40 51 10
NC_001416.1 51 52 11
NC_001416.1 52 56 12
NC_001416.1 56 59 13
NC_001416.1 59 62 14
NC_001416.1 62 63 15
NC_001416.1 63 64 16
NC_001416.1 64 66 17
NC_001416.1 66 73 18
NC_001416.1 73 78 19
Long insert libraries can be used to validate the correctness of contigs assembled using short reads. A drop of physical coverage indicates a misassembly in the contig, as depicted in the plot below, coming from the sequencing of the microalga Nannochloropsis gaditana.
