Usage

Using Enly is very simple, the user has only to specify a series of parameters once, and then all the following steps are performed automatically by the script.

Enter the folder genome created during the installation, and then, from the command line:

$ perl enly.pl -i fasta file with contigs -b bases to detach -r reference genome fasta file -s alignment length threshold

Most of the options are self-explanatory:
fasta file with contigs is the multiFASTA file featuring all the contigs you want to enlarge,
bases to detach is the maximum number of bases to detach from each extremity of the contigs. For 454 sequencing, 500 bases can be a good starting point,
reference genome fasta file is the FASTA file with the reference genome,
alignment length threshold is the minimum percentage of alignment between the contig and the reads that Enly joins at the extremities. For a very safe enlargement (that, howaver, can lead you to miss significant matches) you can use 99 or 98. To avoid false positives, you are advised not to go below 80 – 85.