How to reconstruct a genome from a contigs file?

Question

[Elisa]

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

Answer 1

[Joel Wallenius]

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?

[Elisa]

I have 516 contigs of different lengths. Some are about 30000 bases long while others about 100 (these seeming more like reads). Which alignment tool is the most recommended in these cases? Thank you for your reply!

[Joel Wallenius]

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. :)

[Elisa]

Thank you for your help :)

[GenoMax]

Use minimap2 if you want a fast aligner and want to be able to create SAM/BAM files for viewing. Otherwise aligners like lastz or mummer may also be used.

[dthorbur]

You can also use a tool specifically designed for assembling reference genomes via synteny - Chromosemble