Reporting alignment stats
An important step for checking the quality of a particular reference assembly is to
generate depth and breadth of coverage of the reads. A number of tools have been developed
for this.
Depth of coverage
Breadth of coverage
Standard error and covariance
weeSAM
weeSAM takes either a SAM or BAM file
as an input and can generate the output in text-tab delimited format or as an html file with
figures of coverage plots. If a SAM file is provided as input, the BAM file will be automatically produced.