My promotor told to try and do the assembly from the first round of assemblies. What i have are contigs : 1. created using Nanopore reads and assemblied in Canu 2. contigs from Canu corrected with PE reads using Pilon 3. contigs from SPAdes assembly using PE reads 4. contigs from hybrid SPAdes using Nanopore and PE
But my question is how one could do that? And would this really give any better output?
which version of those has the best stats? (N50 etc) . Is it near to the expected?
Can you describe more elaborated what kind of data you all have? seq versions, #reads, coverage, ...
I so sorry for not providing more information. Haploid geenome calculated with k=20 is 13,444,390 bp. As for the coverage I'm actually not sure how to check it especially after using canu and pilon. Should I map the reads back to the assembly? I just recently started with boinformatics so I still don't fully understand everything..
As also pointed out by colindaven , I would go for #2, that one looks already more than decent.
You might indeed investigate though whether you might buff it up even more with the other three.