I have Illumina paired-end/mate-pair reads and I would like to find out the min and max insert size is. For Aligner like SOAP2 is necessary to specify the insert size?
What is the best way to calculate the min and max insert size?
Thank you in advance.
Usually it does not matter too much. Giving the max a large value (e.g. 1000bp for typical Illumina reads) is fine. Or use BWA, which estimates the insert size on the fly.