1. When will genome sequences produced by the IPC become publically available?

Researchers who provided strains have priority access to corresponding genome sequences through personal user accounts on IPCD. They must agree to public release of the data. All genome sequences produced by the IPC will ultimately be deposited in GenBank and included in the Pseudomonas Genomes Database.

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 for a P. aeruginosa genome. 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.