Assembly

[JornBR]

HI Im new in NGS and I have a maybe silly question, I sequenced two isolates of my bacteria of interest and the genome of the reference strain is complete and available. I wonder if it is best to assemble against the reference genome or make a de novo assembly so I don't lose information that maybe is not present in the reference.

Hope someone can help me to take the right option.

[mastal]

If there is a reference genome available, then you can do a reference guided assembly in the first instance.

Bacterial genomes are not very large, so shouldn't require too much in the way of computational resources, so you can try both methods and compare the results.

[Brian Bushnell]

I would encourage you to do a completely de novo assembly. As mastal said, you can easily do this both ways and compare results. But, a purely de novo assembly has less risk of mistakes due to differences from the reference. You can obviously gain more continuity with a reference-guided approach, but you will incur misassemblies, so I don't think it's a good idea.

[gringer]

What platform did you do the bacterial sequencing on? Why do you need to assemble at all (rather than just looking for variants that differ from the reference)?

If a full-length assembly is absolutely required, do you have another $2000 USD to resequence those isolates (and another 10 more) on a rapid barcoded run of a MinION?