Comparing raw fq files with already processed assemblies

[rduarte]

Hey gyus

I am relatively new to next-generation sequencing data, but I have improved a lot in the last period by self-learning and using the information on this forum.

I have a particular question in which I need your help.

I have a lot of yeast strains sequenced by Illumina paired-end, and I have the fastq files that I already know how to process.
Although, I would like to compare my data with data from other projects, but from which I only have or a final table of SNP positions, or the assemblies.
How can I compare both informations?

And also, how can I compare in the case of different yeast species (different reference files)?

Thanks a lot in advance for your help

[GenoMax]

You can use the same exact reference (as the one used for the SNP data) to align your reads and then call SNP's (I will assume that you know how to QC/trim, if needed).

One option would then be to use vcf-compare from VCFTools.

You will want to assemble your own data before comparing assemblies with something like Mauve.

Do you know the zygosity/ploidy of all your strains? Something to be aware of as you do comparisons.