I did I tried to run a workflow to do a bacterial genome assembly of ONT sequences on Galaxy. I did initial raw sequences QC with FastQC and Nanoplot then trimmed using porechop
I then went on to assemly with flye. I suspect there could be important steps that I may have missed. When I tryed to align the sequences using MEGA , instead of seeing an Individual sequence I saw a series of Contig sequences? Did I miss a step ? scafolding or something? How do I correct this ? Whe I apploaded the sequence It showed that Was a V. Cholerae ST 69 impliying a successful assemly
Hi @HGM
We have tutorials here if you would like to look at some examples
You could also scroll to the very bottom of the Flye tool form to find direct links to specific tutorials.
Then for this part
This sounds expected. Even if the target genome is a “single chromosome” you might have trouble getting that complete assembly the first time through. Much will depend on the coverage of your reads, assembly parameters, sometimes special characteristics of that species’ genome … the tutorials above have advice for these cases, along with suggested tools you can use to investigate your assembly result more, and how to refine it more when possible.
You’ll also find example workflow templates in those tutorials, and can find even more here in our Galaxy Published Workflow resources.
- Web Search → GTN Pan-Galactic Workflow Search.
Hope this helps! 