Identifying distance between mate pairs

Question

[onspotproductions]

I would like to know of a few tools for identifying distances between mate pairs on datasets where that is not given.

Answer 1

[Biomonika (Noolean)]

REAPR

picard's CollectInsertSizeMetrics

Answer 2

[h.mon]

You can get a biased estimate by merging overlapping pairs and measuring the resulting sequence sizes, or you can map to a reference genome and estimate insert size. BBMerge can merge reads and output an insert size histogram, BBMap can map and also output an insert size histogram.