For the past month or so I've been using discoSNP++ with test data sets to see if it will work for particular needs. (It works great!!). The test data sets I have been using are 100bp reads. For my future experimental data sets I am wondering about the need for 100bp reads. It would be easier to piggyback my sequencing with other experiments if I used 50bp reads, but I'm wondering about the effect this would have on the efficiency of the program to detect the SNPs I'm looking for. Can you comment on the effects of using 50bp vs 100bp reads (let's assume ~40M reads per set)? If it matters for your answer, I've been using "-b 1 -D 0 -P 1 -k 31 -c 4 -C 2147483647 -d 1"