I have the Illumina reads and assembly of my bacteria from pure culture DNA sequencing and the nanopore sequencing data from the metagenome (DNA of co-culture). Does anyone know the best way to improve the quality of my bacterial genomic assembly?
There are different way to do this and have done by many. Either you can make separate assembly from both of the respective data and final assemblies can be mapped to each other to fill the gaps. Or you can merge the data with specific tools and parameters to generate a hybrid assembly. There are several methods/tools out there to do it. You will get enough references for "how to do it" thing.
Hi Carla S Vizzotto although I dont have experience scaffolding an illumina assembly with nanopore data but I know that people have used software like LINKS: https://github.com/bcgsc/LINKS which are designed to do just this
Hi Carla S Vizzotto ,
I would suggest to look into SPAdes. It allows the generation of hybrid assemblies using Illumina and Nanopore datasets.
Article SPAdes: A New Genome Assembly Algorithm and Its Applications...
https://cab.spbu.ru/files/release3.15.0/manual.html#sec3.3
- Badges
- Science method