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I started Lineus ruber transcriptome assembly with Casey’s pipeline AGALMA. Since velvet was not compiled with multithread capabilities and oases is not multithreaded it was taking too long (24h). I then stopped it and managed to start an assembly with CLC. With the following parameters:

Automatic word size = ON
Automatic bubble size = ON
Minimun contig length = 170
Perform scaffolding = OFF
Map reads back = ON
  mismatch = 2
  insertion = 3
  deletion = 3
  length = 0.5
  similarity = 0.8
Global alignment = OFF
Update contigs = ON
Creat list of un-mapped = OFF

It started at 21h30 and finished ~06h00 in the next morning.