Which softwares are the best for this work? What is the maximum no of genomes a software can allow me to compare together? Is there any smart way to do this? Like maybe, some big data analytical or data science related approaches to go about the same?
Kindly help me with this by providing your inputs. This is a college project.
Thank you
I suggest you annotate your genomes using Prokka ( https://github.com/tseemann/prokka ) and use the annotated GFF3 files to generate a comparative analysis of the presence/absence of all the genes using Roary ( https://sanger-pathogens.github.io/Roary/ )
This would give you a core genome with all the genes that are shared between all your genomes, as well as an accessory genome to highlight which genes are unique to some groups of your population
How did you generate the genomes? or did you sequence the genomes or you are trying to use the data from databases for your interpretation?
Also, if you have the paired-end reads you could use Nullarbor ( https://github.com/tseemann/nullarbor ) for a complete and comprehensive analysis. Its not easy to install but its worth it.
On the other hand, if you want to make a SNP analysis you could use Snippy (https://github.com/tseemann/snippy).
To quickly compare your genomes you can apply Mash and use the obtained pair-wise sequences to cluster them.
If you have any kind of phenotype data and want to perform a GWAS study, you can use k-mer based approaches (e.g. SEER).
You could also try pan-genomic approaches. E.g. Roary can handle many bacterial genomes, and there are also other similar tools for this task and further downstream analyses.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology
- Virology
- Virus