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.