Padena returns too many sequences

Feb 5, 2015 at 6:43 PM
So I run the Padena util and I'm not sure if I'm missing something, but it always returns more contigs than sequences that I started with. So for example I ran Padena Assemble on a fasta with 500,000 sequences and got back almost 4 million contigs, so it's not even putting the original sequence back together. Am I missing something here because that doesn't seem like it should be expected.
Also, I'm running it with no params, so just "PadenaUtil Assemble file.fa
Apr 19, 2015 at 2:18 AM
Likely a bit too late for an answer, but.....

It is impossible to get more basepairs than you started with, but certainly possible to get more sequences. This is almost certainly caused by being redundant sequences in your program that it cannot put back together after slicing them up. Try increasing the K-mer length (the default is 13, go to 19), you should see many fewer sequences.