NovaSeq Assembly – The Struggle is Real – Real Annoying!

Well, I continue to struggle to makek progress on assembling the geoduck Illumina NovaSeq data. Granted, there is a ton of data (374GB!!!!), but it’s still frustrating that we can’t get an assembly anywhere…

Here are some of the struggles so far:




  • Can’t install one of the dependencies (SOAP error correction)
  • Actually, I need to try the binary version of this, instead of the source version (the source version fails at the make step)

So, next up will trying the following two assemblers:

  • JR-Assembler: Will see if SOAPec binary will work, and then run an assembly.
  • AllPaths-LG: I was able to install this successfully on Mox.

Additionally, we’ve ordered some additional hard drives and will be converting the old head/master node on the Apple Xserve cluster to Linux. The old master node is a little better equipped than the other Apple Xserve “birds”, so will try to re-run Meraculous on it once we get it converted.

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