Hello! In my team we performed genome resequencing. The previous genome assembly (not our team) was obtained from Sanger WGS. We used Illumina to generate paired-end reads with high depth of coverage. After mapping our reads, we have found many indels in the genome that occur next to the previously annotated genes. We found that these indels caused ORF truncations in many cases and the previously annotated genes have incomplete ORFs. Is there any tool/software designed to fix indels in the genome using the mapped resequencing data? After fixing the indels we would like to reannotate the entire genome. Thanks for any hints.