CLC paired read orientation- max. and min. read distance

[gevielr]

When importing data into CLC Genomics Workbench for a de novo assembly (100 bp paired end reads), you are required to input the read orientation minimum and maximum distance between paired reads. How is this calculated?

Initially, I thought the range was calculated by the total size of the fragment. So, if my inserts were 200-220 bp + 120 bp for adaptors, the size of the fragment would be 320-340 bp. The reads being 100 bp on each side, the distance between both would be a minimum distance of 120 bp. However, my assembly using this logic, while OK, had the majority of the paired reads "broken" in the analysis.

After asking around, I was told that the distance shouldn't include the adaptors. So that the minimum distance between 2 reads would be around 0 or an insert size of 200-220 bp?

When I tried this though, the majority of the paired reads were broken in the analysis, and my contigs were generally smaller.

[gevielr]

I should note that I found this in the manual:

"...the paired distance measure that is used throughout the CLC Genomics Workbench is always including the full read sequence. For paired-end libraries it means from the beginning of the forward read to the beginning of the reverse read."

I thought this would mean from the beginning of the transcription of both reads... so 200 bp minimum distance? However, this would not make sense with what I have so far. Could it be possible that they mean from the beginning of the forward reads to the end of the reverse read... so 100 bp minimum distance for a 200 bp insert?

And then how is maximum distance calculated?