Question: Best approach to bacterial hybrid genome assembly

Question

[robert.murphy]

I have PacBio long reads and Illumina short reads and am trying to identify/learn the best method for hybrid assembly. Currently I have identified either using MaSuRCA pipeline or doing the following:

• PacBio based assemblies with Canus (should I correct the pacbio reads first?)

• Polish the Canu assemblies with Illumina reads using Pilon

So my question is what is the best approach and if the use of just Canu and Pilon enough?

Any help would be greatly apriciated :)

[GenoMax]

If you have good quality data just PacBio may be enough for the assembly. Have you done any trials? You should look at SPAdes for the hybrid assemblies as well.

[robert.murphy]

I have not but for educational purposed I want to hybrid assemble anyway. I have looked at SPAdes but was unsure if any preprocessing (such as correction) of the reads (specifically pacbio ones) needed to be done before I run their hybrid pipeline? The documentation says it needs filterd subreads, is my understanding correct that these are just the output of the pacbio sequencing?

[colindaven]

If you just have bacteria Unicycler might do a good job. Available within Galaxy too!