Bowtie2 sequence alignment of Baking yeast

Question

[shaikh.zhas]

I have multiple fastq files of yeast, but as I understoodin order to align those fastq files, I should have reference genome of yeast. However I could find just nucleotide sequence of just separate chromosomes, not whole genome.

So where I can download whole genome of baking yeast?

Answer 1

[Evgeniia Golovina]

You can download whole Ensembl genome here --> ftp://ftp.ensemblgenomes.org/pub/fungi/release-29/fasta/saccharomyces_cerevisiae/dna/

Release 29, Assambly R64-1-1. In README file you can find more info about the dir content.

This is unmasked (i.e. contains all repeats and low complexity regions) ref. genome - Saccharomyces_cerevisiae.R64-1-1.29.dna.toplevel.fa.gz

This one is repeat masked - Saccharomyces_cerevisiae.R64-1-1.29.dna_rm.toplevel.fa.gz. Interspersed repeats and low complexity regions are detected with the RepeatMasker tool and masked by replacing repeats with 'N's.

And soft masked genome - Saccharomyces_cerevisiae.R64-1-1.29.dna_sm.toplevel.fa.gz. Interspersed repeats and low complexity regions are detected with the RepeatMasker tool and masked by replacing repeats with a lower-cased version of the sequence.

Also, there is a Saccharomyces genome database (SGB) - http://www.yeastgenome.org/