Weak Connections

[Ferdi]

Hi -

Thanks a lot for your past help on this forum. I would appreciate if I could have some input on another issue. I have 3 mate-pair libraries and 2 of them don't help much for scaffolding: in the scaffolding log (attached) it doesn't look like n50 increase after they are processed. I previously checked their size distribution and duplication rate, and these parameters do not explain this discrepancy. The main difference between these libraries seems to be the number of 'weak connections': the one that improve the assembly has ~60% weak ratio, the other around 99-100%. Could you please tell me to what do these 'weak connection' correspond to, and whether this is a library quality issue or a a computational issue. 

Thanks a lot for the support!

Best

Ferdi

***************************
For insert size: 3000
 Total PE links                21367069
 PE links to masked contigs    8276783
 On same scaffold PE links     261
Cutoff of PE links to make a reliable connection: 5
Report from checkScaf: 0 scaffold segments broken.
Add large insert size PE links: 44 orientation-conflict links, 184 contigs acrossed by normal links.
 Active connections    21266560
 Weak connections      21346238
 Weak ratio            100.4%
0 circles removed.

***************************
For insert size: 5000
 Total PE links                6715557
 PE links to masked contigs    3881080
 On same scaffold PE links     92688
Cutoff of PE links to make a reliable connection: 5
Report from checkScaf: 15 scaffold segments broken.
Add large insert size PE links: 171129 orientation-conflict links, 79940 contigs acrossed by normal links.
 Active connections    3275254
 Weak connections      1984346
 Weak ratio            60.6%
5546 circles removed.

***************************
For insert size: 6000
 Total PE links                21203082
 PE links to masked contigs    11410261
 On same scaffold PE links     829
Cutoff of PE links to make a reliable connection: 5
Report from checkScaf: 0 scaffold segments broken.
Add large insert size PE links: 134 orientation-conflict links, 410 contigs acrossed by normal links.
 Active connections    3690566
 Weak connections      3683960
 Weak ratio            99.8%
4048 circles removed.