<p>I am still new to bioinformatics and I have not yet fully understood the definition of contig. I have read a few explanations and what I understand is that contigs are fragments of the genome for which we are certain that the order of the bases is correct. Then, we make scaffolds out of the contigs and the goal is to get one scaffold to represent the entire genome.</p>

<p>Right now, I am trying to obtain the full reference genome in FASTA format of Streptococcus pneumoniae BR1064. I found <a href="http://www.ebi.ac.uk/ena/data/view/GCA_000203735#WGS%20Sets_GCA_000203735.2">this</a> at ENA and in the top right category under &quot;Send Feedback&quot; it appears &quot;Genome Representation: full&quot;. From there, one can get over to the <a href="http://www.ebi.ac.uk/ena/data/view/AFBZ01000001-AFBZ01000245">assembly contig</a> and there are 245 contigs. Can I just put all this contigs together and obtain the full genome of the organism? If so, is there a particular way to do it? Should it just be in increasing numerical order?</p>

You're right that contigs are just fragments of the genome, and that scaffolding is the next step in assembly. Usually, this is done using genetic maps and SNPs (or other markers) so that the contigs can be anchored along that genetic map. Here's one recent example with the *Brassica oleracea* genome: [The *Brassica oleracea* genome reveals the asymmetrical evolution of polyploid genomes][1]

Looking at the [publication][2] for your genome, it doesn't look like they performed scaffolding, maybe because there is nothing to use as a reference to scaffold against. Therefore, it is likely that the 245 contigs are just numbered by the order they fell out of the assembly program, an order which doesn't reflect the 'real' genome. In that case, I wouldn't concatenate them.

What do you want to do with the contigs? If it's just SNP calling or something like that, I would leave the sequences as contigs.

 [1]: http://www.nature.com/ncomms/2014/140523/ncomms4930/full/ncomms4930.html#methods
 [2]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133277/