Detecting and correcting mis-assembled reads in contigs

De novo assemblies do not have the possibility of quality control with an external sequence. In fact, accuracy and reliability of these assemblies is highly affected by sequencing errors and mis-assemblies. Here, a frequencybased algorithm is developed in Ruby and intended to discern assembly errors from polymorphisms/read errors and then edit or remove the misassembled read(s) to provide more but highly reliable contigs. The software reads and writes the ACE assembly format. Transcriptome and genome assemblies were tested.