I'm using SOAPDenovo-trans to try and assemble a transcriptome with various kmer sizes and multiple assembly programs. I have already used the SOAPDenovo-Trans-31 executable succesfully with a kmer size of 25. It took two days to perform the full assembly. However, with the same configuration and same reads, the SOAPDenovo-Trans-127, with a kmer size of 35 has already been running for two weeks, and I'm talking only about the fastq reading step. As more reads are read, it gets slower, and it's now almost stuck on the last 20.000.000 reads.
Maybe is something abount the RAM. I've got only 58GB to my disposal but, at the same time, I doubt that the 127 version requires so much more memory in comparison.
Have anyoune had this problem before? Are there solutions or alternatives?