Comments (4)
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
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Thanks for your quick response.
- I did not see any error message reported in the log file.
- are you suggesting to use CANU corrected reads or trimmed reads?
- will try -k 15 and keep you posted
from smartdenovo.
RE 2: yes, try CANU
from smartdenovo.
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.
from smartdenovo.
Related Issues (20)
- Died at ./smartdenovo-master/smartdenovo.pl line 23. HOT 6
- Does it support fa.gz as the input? HOT 4
- Nanopore sequence commands HOT 5
- aarch64 platform support
- prefix.dmo.lay.utg and contig.fasta HOT 5
- Assembly versus genome size HOT 2
- how to adjusting parameters to improve the assembly result HOT 3
- so looong!! HOT 1
- .gfa file produced HOT 1
- Resume HOT 1
- Does it support multiple input files like input*.fa ? HOT 1
- Does smartdenovo apply to PacBio HiFi Reads? HOT 2
- Slurm exit code 2 HOT 3
- Assembly summary
- The tool returned zero bytes of wtasm.dmo.cns.log, wtasm.dmo.cns, and wtasm.dmo.lay.utg HOT 1
- make: *** [pwk_genome.mak:27: pwk_genome.dmo.cns] Error 137 HOT 4
- make: *** [JBX.dmo.lay] Error 1 HOT 1
- smartdenovo make error HOT 5
- The assembly of genome is less than expect
- cut_biedge_strgraph_core Undefined references HOT 1
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