I am trying to use ALLPATHS-LG to denovo assemble a bird species genome (~1.1Gb). I prepared 3 libraries, including 350 bp insertion PE libary (60Gb reads), 3kb MP library (30Gb reads) and 8kb MP library (30Gb reads), all are 150 bp PE sequenced.
As you can see, I did not prepared a fragment library for ALLPATHS, so I used soapdenovo2 first, but it always get a much bigger assembly, then I moved to MASURCA, but it always failed before the completion (CA failed). Therefore, I am going to add another 200 bp insertion library and try Allpaths. Hopefully it can work.
Seems like MASURCA need not to trim adapters and remove PE contaminators for mate-pair libraries, do I need to trim adapters and remove PE contaminators for mate-pair libraries before using ALLPATHS?