Performance improvement

[tangerzhang]

Performance improvement

[ruanjue]

Hard to say what exactly happened. Possible ways to fix it:
1, check your log file, is there anything wrong, like segfault
2, try polish raw reads using canu, and then assemble them by SMARTdenovo
3. Nanopore reads are likely to have less k-mer matched, the default parameters were trained for PacBio RSII dataset three years ago. I suggest you to try to use -k 15 to get the alignments again. I haven't run SMARTdenovo on nanopore data yet, if it has good luck, please be kind to tell me.

Best,
Jue

[tangerzhang]

Thanks for your quick response.

1. I did not see any error message reported in the log file.
2. are you suggesting to use CANU corrected reads or trimmed reads?
3. will try -k 15 and keep you posted

[ruanjue]

RE 2: yes, try CANU

[tangerzhang]

I think I have solved the problem. I used CANU corrected reads and tried the two k values: K=15 and K16, leading to two quite different assemblies, 172 Mb and 320 Mb, respectively.
K16 assembly is comparable to estimated genome size (350 Mb) and BUSCO analysis showed it is more reasonable. I will take -k 16.
Thanks again for your suggestion.