The Salmonella Foodborne Syst-OMICS database


1. When will genome sequences from SalFoS become publically available?

Strain providers have priority access to corresponding genome sequences through personal user accounts. They must agree to public release of the data. All genome sequences will ultimately be deposited in GenBank.


2. How are draft genome sequences assembled from raw data? What do scaffolds represent?

Using an Illumina MiSeq instrument, we produce paired-end reads in the form of 2 “fastq” files per strain. These are assembled de novo using the A5 pipeline (Tritt etal. 2012 Plos ONE), which typically results in 20 to 60 scaffolds. Scaffolds, in this case, are large unordered genome fragments. It is reasonable to assume that the complete genome of a strain is present in its “final.scaffolds.fasta” file.


3. How can I obtain annotations for one or more genomes?

For one or a few genomes, we recommend online tools such as RAST or PATRIC. For larger datasets, you might want to consider installing Prokka