Automatic scaffolding with ease.

ScaMPI features a simple and robust algorithm for automatic scaffolding,
developed to extend scaffold only in unambiguous regions to be conservative.
You can watch a video screencasting the process.

Flow chart

Step1: mate pairs alignment

Alignment of mate paired reads against contigs is a trivial yet crucial step for scaffolding. We use PASS, and then "PASS pair" to perform this step. At the end we'll focus on the list of uniquely aligned pairs falling into different contigs.

Step2: creation of arcs

Clustering the alignments we can create connections between contigs, as well as removing the background noise generated by chimeric molecules. The output of this step is stored into a MySQL table for fast data retrieval.

Step3: manual scaffolding

Once that the web interface is ready, you can test the quality of the dataset trying to perform some manual scaffolding.
Tip: from the interface you can launch thes scaffolding from a single contig (seed).

Step4: automatic scaffolding

From the web interface (or from the command line, if you prefere) you can start the automatic scaffolding in the whole genome. This step requires some minutes on a ~100Mb genome with a desktop computer. Results are stored in the database and immediately available from the interface.