Second assembly from existing contigs

Question

[likoo27]

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?

[lieven.sterck]

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, ...

[likoo27]

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..

1. #contigs 57, total length 15353986, %GC 48.87, N50 1113526, L50 5, complete BUSCO 73,79%
2. #contigs 57, total length 15422215, %GC 48.94, N50 1118589, L50 5, complete BUSCO 94,83%
3. #contigs 9297, total length 21499633, %GC 49.04, N50 3765, L50 1349, complete BUSCO 83.79%
4. #contigs 3416, total length 21499633, %GC 48.98, N50 28419, L50 188, complete BUSCO 97.24%

[lieven.sterck]

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.

Answer 1

[colindaven]

Theres a tool called metassembler which might help you out.

https://github.com/biol7210-genomes/assemblers/blob/master/metassembler.md

However, it's a difficult and inherently biased undertaking. I'd try to pick the two most complete assemblies for use. I.e. #2 and #4

Actually, #2 looks pretty decent by itself. Why not try to orientate this to a reference genome if one exists using a tool like Medusa ?

[likoo27]

Thank you, I will check out those tools