[antifolate]

Did you check this? http://www.ncbi.nlm.nih.gov/bioproje...rm=PRJNA169002

I felt there's something missing, but didn't really know what WGS is. Aren't the raw reads all I need?

[GenoMax]

Did you check this? http://www.ncbi.nlm.nih.gov/bioproje...rm=PRJNA169002

I felt there's something missing, but didn't really know what WGS is. Aren't the raw reads all I need?

That link is just the main "project" page (it also appears to be for S. cerevisiae N85 strain). If the "whole genome sequencing" (WGS) data for YHJ7 was submitted under that project it should have been linked there.

See related examples here: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA282006 or http://www.ncbi.nlm.nih.gov/bioproject/PRJNA188959

[antifolate]

If you click Taxonomy in the upper right corner, then Nucleotide on the next page, then WGS CBYJ010000001-CBYJ010000371 on the next one, you'll get here http://www.ncbi.nlm.nih.gov/Traces/w...CBYJ01#contigs where you can download the assembled contigs.

Any tips on hybrid de novo/ reference guided assembly without CLC?

[Brian Bushnell]

You can probably get similar results to a reference-guided assembly by assembling your reads with a normal assembler, then scaffolding with simulated long-mate-pairs from the reference. SSPace is one program for scaffolding assembled contigs. You can generate a fake long-mate-pair library using RandomReads (distributed with BBMap).

Hard to say which assembler you should be using, but Velvet is pretty straightforward and fast, so it's good to try at first.

[antifolate]

I'm confused so please bear with me. I have three files now: lab_S_cervaise.fastq, ricewine_S_cervaise.fastq, and the WGS contigs file (.fsa_nt). What is the WGS file for? Which on of these should I use to assemble the genome?

[GenoMax]

@antifolate: I have not read the paper you linked but the WGS sequence you downloaded from the taxonomy link is for strain N85. How it relates to YHJ7 is something you will need to consider.

[GenoMax]

I'm confused so please bear with me. I have three files now: lab_S_cervaise.fastq, ricewine_S_cervaise.fastq, and the WGS contigs file (.fsa_nt). What is the WGS file for? Which on of these should I use to assemble the genome?

Just a guess. lab = S288c, ricewine = N85 (or YHJ7?).

What is in the WGS contigs file? Just fasta sequence?

[antifolate]

I contacted one of the authors and it turns out they didn't upload the raw reads for the genome sequencing, only the RNA-Seq ones. Thanks all.