Setup

Enly is designed to run on any recent GNU / Linux system with the necessary dependencies installed:

• GNU Compiler Collection (GCC), installed by default on most Linux distros
  http://gcc.gnu.org
• Perl, installed by default on most Linux distros
  http://www.perl.org
• Python, installed by default on most Linux distros
  http://www.python.org
• Phrap, this is the only dependency of Enly not readily available on the web. You have to request a (free) copy of the source code at http://www.phrap.org/phredphrapconsed.html
• MUMmer
  http://mummer.sourceforge.net/
• Primer 3
  http://primer3.sourceforge.net/
• BLAST+
  http://blast.ncbi.nlm.nih.gov/Blast.cgi
• EMBOSS
  http://emboss.sourceforge.net/
• Artemis Comparison Tool
  http://www.sanger.ac.uk/resources/software/act/

To use Enly, you have to run install.sh script (in the main folder), and then follow the on-screen instructions.
Installing Enly means that it is created a folder set up for the elongation of contigs.
Every time you have a set of reads/contigs/reference genome to use, you have to run install.sh.

During the installation, you will be asked for these pieces of information:

• The path of the file, in FASTA format, to be used as the database. This file should contain all the 454 (or Illumina) reads that Enly will look up during its runs.
• Whether you want to use MPI or not during the steps that requires Phrap. If you choose to use the MPI implementation, you will be able to take advantage of your multi-core system more proficiently. You will need the package openMPI installed (query your package manager database for its exact name in your distro).

To run Enly, you will also need:

• A multiFASTA file featuring all the contigs you want to enlarge. These contigs usually come from the draft assemblage of the reads you use as the database.
• A FASTA file with (complete) genome you want to use as a reference. This usually belongs to a different strain of the same species, or to a closely related species.