Abstract
Background: For discovering antibiotic resistant genes in functional genomics, comprehensive variant detection between target genome and template genome is important especially variant on an annotated genes. While Next-generation sequencing (NGS) of high throughput DNA sequencing (DNA-seq) has emerged as a powerful technology to conquer these problems, the success of each assembled tool are dependent upon the availability and quality of detected genes. Results: Here, we describe IRAP (An Iterative Reference-guided Assembly Pipeline for next generation sequencing DNA-seq analysis), a pipeline that assemble reads into contigs and predict gene models by designing an iterative re-sequencing and integrating de novo assembly of DNA-seq data. We have simulate five distinct Helicobacter pylori lineages generated by ART by IRAP assembly pipeline and applied to real data of three Helicobacter pylori isolate pairs and compared the results to the several existing assembly tools. The contigs produced by IRAP has highly accurate (over 99%) and reconstruct more full-length genes for the majority of the existing reference gene sets (100%). All results showed that IRAP can match or outperform than current popular assemblers. Conclusions: These results demonstrate that the IRAP pipeline is able to reconstruct more full-length genes accurately and has more chance to discover potential genes which associate to antibiotic-resistant directly or indirectly.