Hi everyone, I am taking my first steps in bioinformatics and have been assigned a project entitled: Reconstruction of a yeast genome. The source material is a file containing a series of contigs in FASTA format. They come from a genome sequencing of a S. cerevisie strain that was done years ago. The raw files have been lost and this file is all that remains. I was wondering what would be the best way to proceed. Thank you very much for your help
1 answer
Yeast has 16 chromosomes. If you have 16 contigs in that FASTA file, there's not much left to do, methinks.
If you have more than 16 contigs, I think the next step is to align them to a reference genome, thus giving you scaffolds rather than contigs. In the end, you'd have 16 scaffolds containing NNN segments. Is this what reconstruction might mean to you?
I don't know, there are probably many decent ones. For example: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6
If you have time, you could try different ones and compare the results. :)
You can also use a tool specifically designed for assembling reference genomes via synteny - Chromosemble
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