The clc_agp_join Program

When using the -f option in the de novo assembler for outputting scaffold annotations in AGP format, scaffolded contigs are output as individual contigs and not as a single scaffold with N's inserted in between contigs. The AGP file which is generated contain information on scaffolded contigs and the size of gaps that separate contigs in a scaffold. This program takes a list of contigs and an AGP file as input and output a list of contigs where each contig represents a scaffold where contigs are separated with a number of N's corresponding to the gap size. That is, the output of this program is identical with the default output of the de novo assembler.

Further details can be found in Options for All Programs.