A user friendly interface for the whole project.

A major advantage of using ScaMPI for de novo sequencing project is its intuitive and user friendly interface.
Being web based you can install it into any *AMP server (a web server with Apache, MySQL and PHP) and make it available to all project coworkers.

A definite advantage of a web interface is that many computer can access is.

Scampi interface

Home Page

The home page lists contigs and (after performing the scaffolding step) scaffolds, indicating the progress of work in terms of bases in scaffold.

Contig page

For each contig you'll see its properties (size, coverage...) and the connection starting from it. This is a handy tool to perform manual scaffolding, refine existing scaffolds or inspect critical regions.

Tools

The top bar allows accessing tools such as the online BLAST or the scaffolding program itself. Being modular it's possible to extend its core functionalities with plug-ins.

Try it yourself

A limited installation of ScaMPI is available on this site. You'll see how to browse contigs and scaffolds: click here.