I am using cap3 for assembling my 454 RNA-seq reads. It turns out the unparallelized cap3 is too slow (already taking 10 days) given the size of my data (300MB), and I am thinking of using pcap instead of cap3 for my assembly.
However, I am not sure whether it's justifiable to use pcap instead of cap3 for EST assembly, since pcap is a genome assembler. Is there any assumption in pcap violating the principle of EST assembly?
Thanks,
Hao
However, I am not sure whether it's justifiable to use pcap instead of cap3 for EST assembly, since pcap is a genome assembler. Is there any assumption in pcap violating the principle of EST assembly?
Thanks,
Hao