PAGIT - Post Assembly Genome Improvement Toolkit

Tools to generate automatically high quality sequence by ordering contigs, closing gaps, 

correcting sequence errors and transferring annotation.

PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed:

1. ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference.
2. IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.
3. iCORN, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly.
4. RATT, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.