hi, I've been using SSPACE with our internally made mate pair libraries to scaffold a set of E coli contigs. It seems that SSPACE is using only a few thousand of the mate pair reads to perform the scaffolding, and my question is whether that low number is related to the required linkage parameters? My mate pair libraries have a have 100,000 - 2 million paired reads, but that's probably overkill for the purpose of scaffolding 195 contigs?
thx for any help/comments!
-Scott
thx for any help/comments!
-Scott
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