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 <https://github.com/centre-for-virus-research/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.