Integrated Prokaryotic Analysis Pipeline Based On Next-generation Sequencing Technology

The amount of new sequencing data arising from next-generation prokaryotic genomes projects has increased demanding on an integrated pipeline for the analysis and the management of these massive data. A number of genome annotation and transcriptome analysis pipelines for prokaryotic organisms have been developed in the past few years. There is a relative scarcity of combined genome and transcriptome analysis pipelines now. However, there is no an integrated and comprehensive automatic analysis pipeline available to analyzing prokaryotic next-generation sequencing (NGS) data in public field. Our system, which is well designed and integrated genome and transcriptome automatic analysis pipeline, has been developed to fill this gap. Our pipeline is composed of three parts in biological analysis:(i) genome analysis, including gene finding and function predicting. In this part, we have integrated a number of public bioinformatics software to search for protein-coding genes, RNA genes and other functional elements within a genome based on the existing research work. The genome data is returned as a colorful circle map and detailed textual information of genome features.(ii) transcriptome data analysis, including gene expression profiling, differentially expressed genes with functional analysis, detection of transcription start site (TSS), untranslated regulatory regions and intergenic region analysis. Transcriptome analytical methods are mainly created by our own. The transcriptome data is returned as graphical maps of single nucleotide coverage and detailed textual contents.(iii) integrated genome and transcriptome analysis, including verification of previously predicted operon structures and refined annotation. The purpose of this part is to improve the annotation of genome and return detailed verification or correction of predicted gene structure and operons. Additionally, the genome and transcriptome sequence data of Helicobacter pylori strain26695were used to test our automatic analysis pipeline and the results suggested our integrated pipeline is effective for analyzing of prokaryotic genome and transcriptome. Finally, Methanolobus psychrophilus R15finished in our laboratory was used as an example to show the analysis results of our pipeline.