GAPPadder: A sensitive approach for closing gaps on draft genomes with short sequence reads

Abstract

Closing gaps in draft genomes is an important post processing step in genome assembly. At present, most assembled genomes contain gaps. Usually, genomes assembled from short reads or hybrid (with both short and long reads) have much more gaps than genomes assembled purely from long reads (with high coverage). A more complete genome is highly desirable since it leads to better annotation, less genotyping error and easier identification of causal variation associated with traits [1]. Several tools [2]-[4] have been developed for closing gaps on draft genomes with short reads. While these approaches have been used to close gaps, these tools still cannot close many gaps (especially those originated in more complex genomic regions, e.g. repeats).