NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads.

NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads. Adv Exp Med Biol. 2018;1052:39-49 Authors: Kulsum U, Kapil A, Singh H, Kaur P Abstract Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species. It can also assist in identifying drug targets and proposing vaccine candidates. The effective analysis of these large genome datasets necessitates the development of robust tools. Current methods to develop pan-genome do not support direct input of raw reads from the sequencer machine but require preprocessing of reads as an assembled protein/gene sequence file or the binary matrix of orthologous genes/proteins. We have designed an easy-to-use integrated pipeline, NGSPanPipe, which can directly identify the pan-genome from short reads. The output from the pipeline is compatible with other pan-genome analysis tools. We ...
Source: Adv Data - Category: Epidemiology Authors: Tags: Adv Exp Med Biol Source Type: research