The Picard (citation) library is used in SeqSphere+ to process SAM/BAM files. It also provides functions to calculate metrics for validating library construction including the insert size distribution.

Insert Sizes Histogram
Example result of an insert size analysis

The menu function Tools | Genome Utilities | llumina Insert Sizes (Picard) can be used to analyze the distribution of insert sizes of aligned reads. When invoked the SAM/BAM file that should be analyzed must be selected. After the file reading has finished, a windows is opened showing a histogram for the distribution of insert sizes for all reads. Below the histogram the statistical values for mean, standard deviation, median, and mode are shown.

Doc-info.pngHint: This function expects a SAM/BAM file with aligned reads. To analyze the insert size of unaligned reads (i.e, FASTQ files), they must first be mapped to a reference.